diff --git a/README.md b/README.md index 26d543a..953182e 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,16 @@ -# CTD2Galaxy +# CTDConverter - -Given one or more CTD files, `CTD2Galaxy` generates the needed Galaxy wrappers to include them in a Galaxy instance. +Given one or more CTD files, `CTD2Converter` generates the needed wrappers to include them in workflow engines, such as Galaxy and CWL. ## Dependencies -`CTD2Galaxy` has the following python dependencies: +`CTDConverter` relies on [CTDopts]. The dependencies of each of the converters are as follows: -1. `lxml`. -1. [CTDopts] +### Galaxy Converter +- Generation of Galaxy ToolConfig files relies on `lxml` to generate nice-looking XML files. + +## Installing Dependencies You can install the [CTDopts] and `lxml` modules via `conda`, like so: ```sh @@ -22,340 +23,16 @@ Of course, you can just download [CTDopts] and make it available through your `PYTHONPATH` environment variable. To get more information about how to install python modules, visit: https://docs.python.org/2/install/. -## How to install CTD2Galaxy +## How to install CTDConverter -1. Download the source code from https://github.com/genericworkflownodes/CTD2Galaxy. +1. Download the source code from https://github.com/genericworkflownodes/CTDConverter. -## How to use: most common tasks +## Usage -The generator takes several parameters and a varying number of inputs and outputs. The following sub-sections show how to perform the most common operations. +Check the detailed documentation for each of the converters: -Running the generator with the `-h/--help` parameter will print extended information about each of the parameters. +- [Generation of Galaxy ToolConfig files](galaxy/README.md) -### Macros - -Galaxy supports the use of macros via a `macros.xml` file (`CTD2Galaxy` provides a sample macros file in [macros.xml]). Instead of repeating sections, macros can be used and expanded. If you want fine control over the macros, you can use the `-m` / `--macros` parameter to provide your own macros file. - -Please note that the used macros file **must** be copied to your Galaxy installation on the same location in which you place the generated *ToolConfig* files, otherwise Galaxy will not be able to parse the generated *ToolConfig* files! - -### One input, one output - -In its simplest form, `CTD2Galaxy` takes an input CTD file and generates an output Galaxy *ToolConfig* file. The following use of `CTD2Galaxy`: - - $ python generator.py -i /data/sample_input.ctd -o /data/sample_output.xml - -will parse `/data/sample_input.ctd` and generate a Galaxy tool wrapper under `/data/sample_output.xml`. The generated file can be added to your Galaxy instance like any other tool. - -### Converting several CTDs at once - -When converting several CTDs, the expected value for the `-o`/`--output` parameter is a folder. For example: - - $ python generator.py -i /data/ctds/one.ctd /data/ctds/two.ctd -o /data/generated-galaxy-stubs - -Will convert `/data/ctds/one.ctd` into `/data/generated-galaxy-stubs/one.xml` and `/data/ctds/two.ctd` into `/data/generated-galaxy-stubs/two.xml`. - -You can use wildcard expansion, as supported by most modern operating systems: - - $ python generator.py -i /data/ctds/*.ctd -o /data/generated-galaxy-stubs - -### Generating a tool_conf.xml file - -The generator supports generation of a `tool_conf.xml` file which you can later use in your local Galaxy installation. The parameter `-t`/`--tool-conf-destination` contains the path of a file in which a `tool_conf.xml` file will be generated. - - $ python generator.py -i /data/ctds/*.ctd -o /data/generated-galaxy-stubs -t /data/generated-galaxy-stubs/tool_conf.xml - - -## How to use: parameters in detail - -### A word about parameters taking list of values - -All parameters have a short and a long option and some parameters take list of values. Using either the long or the short option of the parameter will produce the same output. The following examples show how to pass values using the `-f` / `--foo` parameter: - -The following uses of the parameter will pass the list of values containing `bar`, `blah` and `blu`: - - -f bar blah blu - --foo bar blah blu - -f bar -f blah -f blu - --foo bar --foo blah --foo blu - -f bar --foo blah blu - -The following uses of the parameter will pass a single value `bar`: - - -f bar - --foo bar - -### Schema validation - -* Purpose: Provide validation of input CTDs against a schema file (i.e, a XSD file). -* Short/long version: `v` / `--validation-schema` -* Required: no. -* Taken values: location of the schema file (e.g., CTD.xsd). - -CTDs can be validated against a schema. The master version of the schema can be found under [CTDSchema]. - -If a schema is provided, all input CTDs will be validated against it. - -### Input file(s) - -* Purpose: Provide input CTD file(s) to convert. -* Short/long version: `-i` / `--input` -* Required: yes. -* Taken values: a list of input CTD files. - -Example: - -Any of the following invocations will convert `/data/input_one.ctd` and `/data/input_two.ctd`: - - $ python generator.py -i /data/input_one.ctd -i /data/input_two.ctd -o /data/generated - $ python generator.py -i /data/input_one.ctd /data/input_two.ctd -o /data/generated - $ python generator.py --input /data/input_one.ctd /data/input_two.ctd -o /data/generated - $ python generator.py --input /data/input_one.ctd --input /data/input_two.ctd -o /data/generated - -The following invocation will convert `/data/input.ctd` into `/data/output.xml`: - - $ python generator.py -i /data/input.ctd -o /data/output.xml -m sample_files/macros.xml - -Of course, you can also use wildcards, which will be automatically expanded by any modern operating system. This is extremely useful if you want to convert several files at a time. Imagine that the folder `/data/ctds` contains three files, `input_one.ctd`, `input_two.ctd` and `input_three.ctd`. The following two invocations will produce the same output in the `/data/galaxy`: - - $ python generator.py -i /data/input_one.ctd /data/input_two.ctd /data/input_three.ctd -o /data/galaxy - $ python generator.py -i /data/*.ctd -o /data/galaxy - -### Finer control over the tools to be converted - -Sometimes only a set of CTDs in a folder need to be converted. The parameter `-r`/`--required-tools` takes the path a file containing the names of tools that will be converted. - - $ python generator.py -i /data/ctds/*.ctd -o /data/generated-galaxy-stubs -r required_tools.txt - -On the other hand, if you want the generator to skip conversion of some CTDs, the parameter `-s`/`--skip-tools` will take the path of a file containing the names of tools that will not be converted. - - $ python generator.py -i /data/ctds/*.ctd -o /data/generated-galaxy-stubs -s skipped_tools.txt - -The format of these files (`required_tools.txt`, `skipped_tools.txt` in the examples above) is straightforward. Each line contains the name of a tool and any line starting with `#` will be ignored. - -### Output destination - -* Purpose: Provide output destination for the generated Galaxy *ToolConfig* files. -* Short/long version: `-o` / `--output-destination` -* Required: yes. -* Taken values: if a single input file is given, then a single output file is expected. If multiple input files are given, then an existent folder, in which all generated Galaxy *ToolConfig* will be written, is expected. - -Example: - -A single input is given, and the output will be generated into `/data/output.xml`: - - $ python generator.py -i /data/input.ctd -o /data/output.xml - -Several inputs are given. The output is the already existent folder, `/data/stubs`, and at the end of the operation, the files `/data/stubs/input_one.ctd.xml` and `/data/stubs/input_two.ctd.xml` will be generated: - - $ python generator.py -i /data/ctds/input_one.ctd /data/ctds/input_two.ctd -o /data/stubs - - -### Adding parameters to the command line - -* Purpose: Galaxy *ToolConfig* files include a `` element in which the command line to invoke the tool can be given. Sometimes it is needed to invoke your tools in a certain way (i.e., passing certain parameters). For instance, some tools offer the possibility to be invoked in a verbose or quiet way or even to be invoked in a headless way (i.e., without GUI). -* Short/long version: `-a` / `--add-to-command-line` -* Required: no. -* Taken values: The command(s) to be added to the command line. - -Example: - - $ python generator.py ... -a "--quiet --no-gui" - -Will generate the following `` element in the generated Galaxy *ToolConfig*: - - TOOL_NAME --quiet --no-gui ... - - -### Blacklisting parameters - -* Purpose: Some parameters present in the CTD are not to be exposed on Galaxy. Think of parameters such as `--help`, `--debug`, that might won't make much sense to be exposed to final users in a workflow management system such as Galaxy. -* Short/long version: `-b` / `--blacklist-parameters` -* Required: no. -* Taken values: A list of parameters to be blacklisted. - -Example: - - $ python generator.py ... -b h help quiet - -Will not process any of the parameters named `h`, `help`, or `quiet` and will not appear in the generated Galaxy *ToolConfig*. - -### Generating a tool_conf.xml file - -* Purpose: Galaxy uses a file `tool_conf.xml` in which other tools can be included. `CTD2Galaxy` can also generate this file. Categories will be extracted from the provided input CTDs and for each category, a different `
` will be generated. Any input CTD lacking a category will be sorted under the provided default category. -* Short/long version: `-t` / `--tool-conf-destination` -* Required: no. -* Taken values: The destination of the file. - -### Providing a default category - -* Purpose: Input CTDs that lack a category will be sorted under the value given to this parameter. If this parameter is not given, then the category `DEFAULT` will be used. -* Short/long version: `-c` / `--default-category` -* Required: no. -* Taken values: The value for the default category to use for input CTDs lacking a category. - -Example: - -Suppose there is a folder containing several CTD files. Some of those CTDs don't have the optional attribute `category` and the rest belong to the `Data Processing` category. The following invocation: - - $ python generator.py ... -c Other - -will generate, for each of the categories, a different section. Additionally, CTDs lacking a category will be sorted under the given category, `Other`, as shown: - -
- - - ... -
- -
- - - ... -
- -### Providing a path for the location of the ToolConfig files - -* Purpose: The `tool_conf.xml` file contains references to files which in turn contain Galaxy *ToolConfig* files. Using this parameter, you can provide information about the location of your tools. -* Short/long version: `-g` / `--galaxy-tool-path` -* Required: no. -* Taken values: The path relative to your `$GALAXY_ROOT/tools` folder on which your tools are located. - -Example: - - $ python generator.py ... -g my_tools_folder - -Will generate `` elements in the generated `tool_conf.xml` as follows: - - - -In this example, `tool_conf.xml` refers to a file located on `$GALAXY_ROOT/tools/my_tools_folder/some_tool.xml`. - - -### Hardcoding parameters - -* Purpose: Fixing the value of a parameter and hide it from the end user. -* Short/long version: `-p` / `--hardcoded-parameters` -* Required: no. -* Taken values: The path of a file containing the mapping between parameter names and hardcoded values to use in the `` section. - -It is sometimes required that parameters are hidden from the end user in workflow systems such as Galaxy and that they take a predetermined value. Allowing end users to control parameters similar to `--verbosity`, `--threads`, etc., might create more problems than solving them. For this purpose, the parameter `p`/`--hardcoded-parameters` takes the path of a file that contains up to three columns separated by whitespace that map parameter names to the hardcoded value. The first column contains the name of the parameter and the second one the hardcoded value. The first two columns are mandatory. - -If the parameter is to be hardcoded only for certain tools, a third column containing a comma separated list of tool names for which the hardcoding will apply can be added. - -Lines starting with `#` will be ignored. The following is an example of a valid file: - - # Parameter name # Value # Tool(s) - threads \${GALAXY_SLOTS:-24} - mode quiet - xtandem_executable xtandem XTandemAdapter - verbosity high Foo, Bar - -This will produce a `` section similar to the following one for all tools but `XTandemAdapter`, `Foo` and `Bar`: - - TOOL_NAME -threads \${GALAXY_SLOTS:-24} -mode quiet ... - -For `XTandemAdapter`, the `` will be similar to: - - XtandemAdapter ... -threads \${GALAXY_SLOTS:-24} -mode quiet -xtandem_executable xtandem ... - -And for tools `Foo` and `Bar`, the `` will be similar to: - - Foo ... ... -threads \${GALAXY_SLOTS:-24} -mode quiet -verbosity high ... - - -### Including additional macros files - -* Purpose: Include external macros files. -* Short/long version: `-m` / `--macros` -* Required: no. -* Default: `macros.xml` -* Taken values: List of paths of macros files to include. - -*ToolConfig* supports elaborate sections such as ``, ``, etc., that are identical across tools of the same suite. Macros files assist in the task of including external xml sections into *ToolConfig* files. For more information about the syntax of macros files, see: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Reusing_Repeated_Configuration_Elements - -There are some macros that are required, namely `stdio`, `requirements` and `advanced_options`. A template macro file is included in [macros.xml]. It can be edited to suit your needs and you could add extra macros or leave it as it is and include additional files. - -Every macro found in the included files and in `support_files/macros.xml` will be expanded. Users are responsible for copying the given macros files in their corresponding galaxy folders. - -### Providing a default executable path - -* Purpose: Help Galaxy locate tools by providing a path. -* Short/long version: `-x` / `--default-executable-path` -* Required: no. -* Taken values: The default executable path of the tools in the Galaxy installation. - -CTDs can contain an `` element that will be used when executing the tool binary. If this element is missing, the value provided by this parameter will be used as a prefix when building the `` section. Suppose that you have installed a tool suite in your local Galaxy instance under `/opt/suite/bin`. The following invocation of the converter: - - $ python generator.py -x /opt/suite/bin ... - -Will produce a `` section similar to: - - /opt/suite/bin/Foo ... - -For those CTDs in which no `` could be found. - - -### Generating a `datatypes_conf.xml` file - -* Purpose: Specify the destination of a generated `datatypes_conf.xml` file. -* Short/long version: `-d` / `--datatypes-destination` -* Required: no. -* Taken values: The path in which `datatypes_conf.xml` will be generated. - -It is likely that your tools use file formats or mimetypes that have not been registered in Galaxy. The generator allows you to specify a path in which an automatically generated `datatypes_conf.xml` file will be created. Consult the next section to get information about how to register file formats and mimetypes. - - -### Providing Galaxy file formats - -* Purpose: Register new file formats and mimetypes. -* Short/long version: `-f` / `--formats-file` -* Required: no. -* Taken values: The path of a file describing formats. - -Galaxy supports the concept of file format in order to connect compatible ports, that is, input ports of a certain data format will be able to receive data from a port from the same format. This converter allows you to provide a personalized file in which you can relate the CTD data formats with supported Galaxy data formats. The format file is a simple text file, each line containing several columns separated by whitespace. The content of each column is as follows: - -* 1st column: file extension, this column is required. -* 2nd column: data type, as listed in Galaxy, this column is optional. -* 3rd column: full-named Galaxy data type, as it will appear on datatypes_conf.xml; this column is required if the second column is included. -* 4th column: mimetype, this column is optional. - -The following is an example of a valid "file formats" file: - - # CTD type # Galaxy type # Long Galaxy data type # Mimetype - csv tabular galaxy.datatypes.data:Text - fasta - ini txt galaxy.datatypes.data:Text - txt - idxml txt galaxy.datatypes.xml:GenericXml application/xml - options txt galaxy.datatypes.data:Text - grid grid galaxy.datatypes.data:Grid - -Note that each line consists of either one, three or four columns. In the case of data types already registered in Galaxy (such as `fasta` and `txt` in the above example), only the first column is needed. In the case of data types that haven't been yet registered in Galaxy, the first three columns are needed (mimetype is optional). - -For information about Galaxy data types and subclasses, consult the following page: https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes - - -## Notes about some of the *OpenMS* tools - -* Most of the tools can be generated automatically. Some of the tools need some extra work (for now). -* These adapters need to be changed, such that you provide the path to the executable: - * FidoAdapter (add `-exe fido` in the command tag, delete the `$param_exe` in the command tag, delete the parameter from the input list). - * MSGFPlusAdapter (add `-executable msgfplus.jar` in the command tag, delete the `$param_executable` in the command tag, delete the parameter from the input list). - * MyriMatchAdapter (add `-myrimatch_executable myrimatch` in the command tag, delete the `$param_myrimatch_executable` in the command tag, delete the parameter from the input list). - * OMSSAAdapter (add `-omssa_executable omssa` in the command tag, delete the `$param_omssa_executable` in the command tag, delete the parameter from the input list). - * PepNovoAdapter (add `-pepnovo_executable pepnovo` in the command tag, delete the `$param_pepnovo_executable` in the command tag, delete the parameter from the input list). - * XTandemAdapter (add `-xtandem_executable xtandem` in the command tag, delete the $param_xtandem_executable in the command tag, delete the parameter from the input list). - * To avoid the deletion in the inputs you can also add these parameters to the blacklist - - $ python generator.py -b exe executable myrimatch_excutable omssa_executable pepnovo_executable xtandem_executable - -* These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in Galaxy-stable: - * SeedListGenerator - * SpecLibSearcher - * MapAlignerIdentification - * MapAlignerPoseClustering - * MapAlignerSpectrum - * MapAlignerRTTransformer [CTDopts]: https://github.com/genericworkflownodes/CTDopts [macros.xml]: https://github.com/WorkflowConversion/CTD2Galaxy/blob/master/macros.xml diff --git a/dist/conda/bld.bat b/dist/conda/bld.bat deleted file mode 100644 index c40a9bb..0000000 --- a/dist/conda/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%PYTHON%" setup.py install -if errorlevel 1 exit 1 diff --git a/dist/conda/build.sh b/dist/conda/build.sh deleted file mode 100644 index 5a5aeeb..0000000 --- a/dist/conda/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install diff --git a/dist/conda/meta.yaml b/dist/conda/meta.yaml deleted file mode 100644 index 175bdb5..0000000 --- a/dist/conda/meta.yaml +++ /dev/null @@ -1,28 +0,0 @@ -package: - name: ctd2galaxy - version: "1.0" - -source: - git_rev: v1.0 - git_url: https://github.com/WorkflowConversion/CTD2Galaxy.git - -build: - noarch_python: True - -requirements: - build: - - python - - setuptools - - run: - - python - - lxml - - ctdopts 1.0 - -test: - imports: - - CTDopts.CTDopts - -about: - home: https://github.com/WorkflowConversion/CTD2Galaxy - license_file: LICENSE diff --git a/galaxy/README.md b/galaxy/README.md new file mode 100644 index 0000000..5363163 --- /dev/null +++ b/galaxy/README.md @@ -0,0 +1,336 @@ +# Conversion of CTD Files to Galaxy ToolConfigs + +## How to use: most common Tasks + +The Galaxy ToolConfig generator takes several parameters and a varying number of inputs and outputs. The following sub-sections show how to perform the most common operations. + +Running the generator with the `-h/--help` parameter will print extended information about each of the parameters. + +### Macros + +Galaxy supports the use of macros via a `macros.xml` file (`CTD2Galaxy` provides a sample macros file in [macros.xml]). Instead of repeating sections, macros can be used and expanded. If you want fine control over the macros, you can use the `-m` / `--macros` parameter to provide your own macros file. + +Please note that the used macros file **must** be copied to your Galaxy installation on the same location in which you place the generated *ToolConfig* files, otherwise Galaxy will not be able to parse the generated *ToolConfig* files! + +### One input, one Output + +In its simplest form, `CTD2Galaxy` takes an input CTD file and generates an output Galaxy *ToolConfig* file. The following use of `CTD2Galaxy`: + + $ python generator.py -i /data/sample_input.ctd -o /data/sample_output.xml + +will parse `/data/sample_input.ctd` and generate a Galaxy tool wrapper under `/data/sample_output.xml`. The generated file can be added to your Galaxy instance like any other tool. + +### Converting several CTDs at once + +When converting several CTDs, the expected value for the `-o`/`--output` parameter is a folder. For example: + + $ python generator.py -i /data/ctds/one.ctd /data/ctds/two.ctd -o /data/generated-galaxy-stubs + +Will convert `/data/ctds/one.ctd` into `/data/generated-galaxy-stubs/one.xml` and `/data/ctds/two.ctd` into `/data/generated-galaxy-stubs/two.xml`. + +You can use wildcard expansion, as supported by most modern operating systems: + + $ python generator.py -i /data/ctds/*.ctd -o /data/generated-galaxy-stubs + +### Generating a tool_conf.xml File + +The generator supports generation of a `tool_conf.xml` file which you can later use in your local Galaxy installation. The parameter `-t`/`--tool-conf-destination` contains the path of a file in which a `tool_conf.xml` file will be generated. + + $ python generator.py -i /data/ctds/*.ctd -o /data/generated-galaxy-stubs -t /data/generated-galaxy-stubs/tool_conf.xml + + +## How to use: Parameters in Detail + +### A Word about Parameters taking Lists of Values + +All parameters have a short and a long option and some parameters take list of values. Using either the long or the short option of the parameter will produce the same output. The following examples show how to pass values using the `-f` / `--foo` parameter: + +The following uses of the parameter will pass the list of values containing `bar`, `blah` and `blu`: + + -f bar blah blu + --foo bar blah blu + -f bar -f blah -f blu + --foo bar --foo blah --foo blu + -f bar --foo blah blu + +The following uses of the parameter will pass a single value `bar`: + + -f bar + --foo bar + +### Schema Validation + +* Purpose: Provide validation of input CTDs against a schema file (i.e, a XSD file). +* Short/long version: `v` / `--validation-schema` +* Required: no. +* Taken values: location of the schema file (e.g., CTD.xsd). + +CTDs can be validated against a schema. The master version of the schema can be found under [CTDSchema]. + +If a schema is provided, all input CTDs will be validated against it. + +### Input File(s) + +* Purpose: Provide input CTD file(s) to convert. +* Short/long version: `-i` / `--input` +* Required: yes. +* Taken values: a list of input CTD files. + +Example: + +Any of the following invocations will convert `/data/input_one.ctd` and `/data/input_two.ctd`: + + $ python generator.py -i /data/input_one.ctd -i /data/input_two.ctd -o /data/generated + $ python generator.py -i /data/input_one.ctd /data/input_two.ctd -o /data/generated + $ python generator.py --input /data/input_one.ctd /data/input_two.ctd -o /data/generated + $ python generator.py --input /data/input_one.ctd --input /data/input_two.ctd -o /data/generated + +The following invocation will convert `/data/input.ctd` into `/data/output.xml`: + + $ python generator.py -i /data/input.ctd -o /data/output.xml -m sample_files/macros.xml + +Of course, you can also use wildcards, which will be automatically expanded by any modern operating system. This is extremely useful if you want to convert several files at a time. Imagine that the folder `/data/ctds` contains three files, `input_one.ctd`, `input_two.ctd` and `input_three.ctd`. The following two invocations will produce the same output in the `/data/galaxy`: + + $ python generator.py -i /data/input_one.ctd /data/input_two.ctd /data/input_three.ctd -o /data/galaxy + $ python generator.py -i /data/*.ctd -o /data/galaxy + +### Finer Control over the Tools to be converted + +Sometimes only a set of CTDs in a folder need to be converted. The parameter `-r`/`--required-tools` takes the path a file containing the names of tools that will be converted. + + $ python generator.py -i /data/ctds/*.ctd -o /data/generated-galaxy-stubs -r required_tools.txt + +On the other hand, if you want the generator to skip conversion of some CTDs, the parameter `-s`/`--skip-tools` will take the path of a file containing the names of tools that will not be converted. + + $ python generator.py -i /data/ctds/*.ctd -o /data/generated-galaxy-stubs -s skipped_tools.txt + +The format of these files (`required_tools.txt`, `skipped_tools.txt` in the examples above) is straightforward. Each line contains the name of a tool and any line starting with `#` will be ignored. + +### Output Destination + +* Purpose: Provide output destination for the generated Galaxy *ToolConfig* files. +* Short/long version: `-o` / `--output-destination` +* Required: yes. +* Taken values: if a single input file is given, then a single output file is expected. If multiple input files are given, then an existent folder, in which all generated Galaxy *ToolConfig* will be written, is expected. + +Example: + +A single input is given, and the output will be generated into `/data/output.xml`: + + $ python generator.py -i /data/input.ctd -o /data/output.xml + +Several inputs are given. The output is the already existent folder, `/data/stubs`, and at the end of the operation, the files `/data/stubs/input_one.ctd.xml` and `/data/stubs/input_two.ctd.xml` will be generated: + + $ python generator.py -i /data/ctds/input_one.ctd /data/ctds/input_two.ctd -o /data/stubs + + +### Adding Parameters to the Command-line + +* Purpose: Galaxy *ToolConfig* files include a `` element in which the command line to invoke the tool can be given. Sometimes it is needed to invoke your tools in a certain way (i.e., passing certain parameters). For instance, some tools offer the possibility to be invoked in a verbose or quiet way or even to be invoked in a headless way (i.e., without GUI). +* Short/long version: `-a` / `--add-to-command-line` +* Required: no. +* Taken values: The command(s) to be added to the command line. + +Example: + + $ python generator.py ... -a "--quiet --no-gui" + +Will generate the following `` element in the generated Galaxy *ToolConfig*: + + TOOL_NAME --quiet --no-gui ... + + +### Blacklisting Parameters + +* Purpose: Some parameters present in the CTD are not to be exposed on Galaxy. Think of parameters such as `--help`, `--debug`, that might won't make much sense to be exposed to final users in a workflow management system such as Galaxy. +* Short/long version: `-b` / `--blacklist-parameters` +* Required: no. +* Taken values: A list of parameters to be blacklisted. + +Example: + + $ python generator.py ... -b h help quiet + +Will not process any of the parameters named `h`, `help`, or `quiet` and will not appear in the generated Galaxy *ToolConfig*. + +### Generating a tool_conf.xml file + +* Purpose: Galaxy uses a file `tool_conf.xml` in which other tools can be included. `CTD2Galaxy` can also generate this file. Categories will be extracted from the provided input CTDs and for each category, a different `
` will be generated. Any input CTD lacking a category will be sorted under the provided default category. +* Short/long version: `-t` / `--tool-conf-destination` +* Required: no. +* Taken values: The destination of the file. + +### Providing a default Category + +* Purpose: Input CTDs that lack a category will be sorted under the value given to this parameter. If this parameter is not given, then the category `DEFAULT` will be used. +* Short/long version: `-c` / `--default-category` +* Required: no. +* Taken values: The value for the default category to use for input CTDs lacking a category. + +Example: + +Suppose there is a folder containing several CTD files. Some of those CTDs don't have the optional attribute `category` and the rest belong to the `Data Processing` category. The following invocation: + + $ python generator.py ... -c Other + +will generate, for each of the categories, a different section. Additionally, CTDs lacking a category will be sorted under the given category, `Other`, as shown: + +
+ + + ... +
+ +
+ + + ... +
+ +### Providing a Path for the Location of the ToolConfig Files + +* Purpose: The `tool_conf.xml` file contains references to files which in turn contain Galaxy *ToolConfig* files. Using this parameter, you can provide information about the location of your tools. +* Short/long version: `-g` / `--galaxy-tool-path` +* Required: no. +* Taken values: The path relative to your `$GALAXY_ROOT/tools` folder on which your tools are located. + +Example: + + $ python generator.py ... -g my_tools_folder + +Will generate `` elements in the generated `tool_conf.xml` as follows: + + + +In this example, `tool_conf.xml` refers to a file located on `$GALAXY_ROOT/tools/my_tools_folder/some_tool.xml`. + + +### Hardcoding Parameters + +* Purpose: Fixing the value of a parameter and hide it from the end user. +* Short/long version: `-p` / `--hardcoded-parameters` +* Required: no. +* Taken values: The path of a file containing the mapping between parameter names and hardcoded values to use in the `` section. + +It is sometimes required that parameters are hidden from the end user in workflow systems such as Galaxy and that they take a predetermined value. Allowing end users to control parameters similar to `--verbosity`, `--threads`, etc., might create more problems than solving them. For this purpose, the parameter `p`/`--hardcoded-parameters` takes the path of a file that contains up to three columns separated by whitespace that map parameter names to the hardcoded value. The first column contains the name of the parameter and the second one the hardcoded value. The first two columns are mandatory. + +If the parameter is to be hardcoded only for certain tools, a third column containing a comma separated list of tool names for which the hardcoding will apply can be added. + +Lines starting with `#` will be ignored. The following is an example of a valid file: + + # Parameter name # Value # Tool(s) + threads \${GALAXY_SLOTS:-24} + mode quiet + xtandem_executable xtandem XTandemAdapter + verbosity high Foo, Bar + +This will produce a `` section similar to the following one for all tools but `XTandemAdapter`, `Foo` and `Bar`: + + TOOL_NAME -threads \${GALAXY_SLOTS:-24} -mode quiet ... + +For `XTandemAdapter`, the `` will be similar to: + + XtandemAdapter ... -threads \${GALAXY_SLOTS:-24} -mode quiet -xtandem_executable xtandem ... + +And for tools `Foo` and `Bar`, the `` will be similar to: + + Foo ... ... -threads \${GALAXY_SLOTS:-24} -mode quiet -verbosity high ... + + +### Including additional Macros Files + +* Purpose: Include external macros files. +* Short/long version: `-m` / `--macros` +* Required: no. +* Default: `macros.xml` +* Taken values: List of paths of macros files to include. + +*ToolConfig* supports elaborate sections such as ``, ``, etc., that are identical across tools of the same suite. Macros files assist in the task of including external xml sections into *ToolConfig* files. For more information about the syntax of macros files, see: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Reusing_Repeated_Configuration_Elements + +There are some macros that are required, namely `stdio`, `requirements` and `advanced_options`. A template macro file is included in [macros.xml]. It can be edited to suit your needs and you could add extra macros or leave it as it is and include additional files. + +Every macro found in the included files and in `support_files/macros.xml` will be expanded. Users are responsible for copying the given macros files in their corresponding galaxy folders. + +### Providing a default executable Path + +* Purpose: Help Galaxy locate tools by providing a path. +* Short/long version: `-x` / `--default-executable-path` +* Required: no. +* Taken values: The default executable path of the tools in the Galaxy installation. + +CTDs can contain an `` element that will be used when executing the tool binary. If this element is missing, the value provided by this parameter will be used as a prefix when building the `` section. Suppose that you have installed a tool suite in your local Galaxy instance under `/opt/suite/bin`. The following invocation of the converter: + + $ python generator.py -x /opt/suite/bin ... + +Will produce a `` section similar to: + + /opt/suite/bin/Foo ... + +For those CTDs in which no `` could be found. + + +### Generating a `datatypes_conf.xml` File + +* Purpose: Specify the destination of a generated `datatypes_conf.xml` file. +* Short/long version: `-d` / `--datatypes-destination` +* Required: no. +* Taken values: The path in which `datatypes_conf.xml` will be generated. + +It is likely that your tools use file formats or mimetypes that have not been registered in Galaxy. The generator allows you to specify a path in which an automatically generated `datatypes_conf.xml` file will be created. Consult the next section to get information about how to register file formats and mimetypes. + + +### Providing Galaxy File Formats + +* Purpose: Register new file formats and mimetypes. +* Short/long version: `-f` / `--formats-file` +* Required: no. +* Taken values: The path of a file describing formats. + +Galaxy supports the concept of file format in order to connect compatible ports, that is, input ports of a certain data format will be able to receive data from a port from the same format. This converter allows you to provide a personalized file in which you can relate the CTD data formats with supported Galaxy data formats. The format file is a simple text file, each line containing several columns separated by whitespace. The content of each column is as follows: + +* 1st column: file extension, this column is required. +* 2nd column: data type, as listed in Galaxy, this column is optional. +* 3rd column: full-named Galaxy data type, as it will appear on datatypes_conf.xml; this column is required if the second column is included. +* 4th column: mimetype, this column is optional. + +The following is an example of a valid "file formats" file: + + # CTD type # Galaxy type # Long Galaxy data type # Mimetype + csv tabular galaxy.datatypes.data:Text + fasta + ini txt galaxy.datatypes.data:Text + txt + idxml txt galaxy.datatypes.xml:GenericXml application/xml + options txt galaxy.datatypes.data:Text + grid grid galaxy.datatypes.data:Grid + +Note that each line consists of either one, three or four columns. In the case of data types already registered in Galaxy (such as `fasta` and `txt` in the above example), only the first column is needed. In the case of data types that haven't been yet registered in Galaxy, the first three columns are needed (mimetype is optional). + +For information about Galaxy data types and subclasses, consult the following page: https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes + + +## Notes about some of the *OpenMS* Tools + +* Most of the tools can be generated automatically. Some of the tools need some extra work (for now). +* These adapters need to be changed, such that you provide the path to the executable: + * FidoAdapter (add `-exe fido` in the command tag, delete the `$param_exe` in the command tag, delete the parameter from the input list). + * MSGFPlusAdapter (add `-executable msgfplus.jar` in the command tag, delete the `$param_executable` in the command tag, delete the parameter from the input list). + * MyriMatchAdapter (add `-myrimatch_executable myrimatch` in the command tag, delete the `$param_myrimatch_executable` in the command tag, delete the parameter from the input list). + * OMSSAAdapter (add `-omssa_executable omssa` in the command tag, delete the `$param_omssa_executable` in the command tag, delete the parameter from the input list). + * PepNovoAdapter (add `-pepnovo_executable pepnovo` in the command tag, delete the `$param_pepnovo_executable` in the command tag, delete the parameter from the input list). + * XTandemAdapter (add `-xtandem_executable xtandem` in the command tag, delete the $param_xtandem_executable in the command tag, delete the parameter from the input list). + * To avoid the deletion in the inputs you can also add these parameters to the blacklist + + $ python generator.py -b exe executable myrimatch_excutable omssa_executable pepnovo_executable xtandem_executable + +* These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in Galaxy-stable: + * SeedListGenerator + * SpecLibSearcher + * MapAlignerIdentification + * MapAlignerPoseClustering + * MapAlignerSpectrum + * MapAlignerRTTransformer + +[CTDopts]: https://github.com/genericworkflownodes/CTDopts +[macros.xml]: https://github.com/WorkflowConversion/CTD2Galaxy/blob/master/macros.xml +[CTDSchema]: https://github.com/genericworkflownodes/CTDSchema \ No newline at end of file diff --git a/galaxy/dist/conda/bld.bat b/galaxy/dist/conda/bld.bat new file mode 100644 index 0000000..c40a9bb --- /dev/null +++ b/galaxy/dist/conda/bld.bat @@ -0,0 +1,2 @@ +"%PYTHON%" setup.py install +if errorlevel 1 exit 1 diff --git a/galaxy/dist/conda/build.sh b/galaxy/dist/conda/build.sh new file mode 100644 index 0000000..5a5aeeb --- /dev/null +++ b/galaxy/dist/conda/build.sh @@ -0,0 +1 @@ +$PYTHON setup.py install diff --git a/galaxy/dist/conda/meta.yaml b/galaxy/dist/conda/meta.yaml new file mode 100644 index 0000000..175bdb5 --- /dev/null +++ b/galaxy/dist/conda/meta.yaml @@ -0,0 +1,28 @@ +package: + name: ctd2galaxy + version: "1.0" + +source: + git_rev: v1.0 + git_url: https://github.com/WorkflowConversion/CTD2Galaxy.git + +build: + noarch_python: True + +requirements: + build: + - python + - setuptools + + run: + - python + - lxml + - ctdopts 1.0 + +test: + imports: + - CTDopts.CTDopts + +about: + home: https://github.com/WorkflowConversion/CTD2Galaxy + license_file: LICENSE diff --git a/galaxy/generator.py b/galaxy/generator.py new file mode 100755 index 0000000..695fdf4 --- /dev/null +++ b/galaxy/generator.py @@ -0,0 +1,1389 @@ +#!/usr/bin/env python +# encoding: utf-8 + +""" +@author: delagarza +""" + + +import sys +import os +import traceback +import ntpath +import string + +from argparse import ArgumentParser +from argparse import RawDescriptionHelpFormatter +from collections import OrderedDict +from string import strip +from lxml import etree +from lxml.etree import SubElement, Element, ElementTree, ParseError, parse + +from CTDopts.CTDopts import CTDModel, _InFile, _OutFile, ParameterGroup, _Choices, _NumericRange, _FileFormat, \ + ModelError, _Null + +__all__ = [] +__version__ = 1.0 +__date__ = '2014-09-17' +__updated__ = '2016-05-09' + +MESSAGE_INDENTATION_INCREMENT = 2 + +TYPE_TO_GALAXY_TYPE = {int: 'integer', float: 'float', str: 'text', bool: 'boolean', _InFile: 'data', + _OutFile: 'data', _Choices: 'select'} + +STDIO_MACRO_NAME = "stdio" +REQUIREMENTS_MACRO_NAME = "requirements" +ADVANCED_OPTIONS_MACRO_NAME = "advanced_options" + +REQUIRED_MACROS = [STDIO_MACRO_NAME, REQUIREMENTS_MACRO_NAME, ADVANCED_OPTIONS_MACRO_NAME] + + +class CLIError(Exception): + # Generic exception to raise and log different fatal errors. + def __init__(self, msg): + super(CLIError).__init__(type(self)) + self.msg = "E: %s" % msg + + def __str__(self): + return self.msg + + def __unicode__(self): + return self.msg + + +class InvalidModelException(ModelError): + def __init__(self, message): + super(InvalidModelException, self).__init__() + self.message = message + + def __str__(self): + return self.message + + def __repr__(self): + return self.message + + +class ApplicationException(Exception): + def __init__(self, msg): + super(ApplicationException).__init__(type(self)) + self.msg = msg + + def __str__(self): + return self.msg + + def __unicode__(self): + return self.msg + + +class ExitCode: + def __init__(self, code_range="", level="", description=None): + self.range = code_range + self.level = level + self.description = description + + +class DataType: + def __init__(self, extension, galaxy_extension=None, galaxy_type=None, mimetype=None): + self.extension = extension + self.galaxy_extension = galaxy_extension + self.galaxy_type = galaxy_type + self.mimetype = mimetype + + +class ParameterHardcoder: + def __init__(self): + # map whose keys are the composite names of tools and parameters in the following pattern: + # [ToolName][separator][ParameterName] -> HardcodedValue + # if the parameter applies to all tools, then the following pattern is used: + # [ParameterName] -> HardcodedValue + + # examples (assuming separator is '#'): + # threads -> 24 + # XtandemAdapter#adapter -> xtandem.exe + # adapter -> adapter.exe + self.separator = "!" + self.parameter_map = {} + + # the most specific value will be returned in case of overlap + def get_hardcoded_value(self, parameter_name, tool_name): + # look for the value that would apply for all tools + generic_value = self.parameter_map.get(parameter_name, None) + specific_value = self.parameter_map.get(self.build_key(parameter_name, tool_name), None) + if specific_value is not None: + return specific_value + + return generic_value + + def register_parameter(self, parameter_name, parameter_value, tool_name=None): + self.parameter_map[self.build_key(parameter_name, tool_name)] = parameter_value + + def build_key(self, parameter_name, tool_name): + if tool_name is None: + return parameter_name + return "%s%s%s" % (parameter_name, self.separator, tool_name) + + +def main(argv=None): # IGNORE:C0111 + # Command line options. + if argv is None: + argv = sys.argv + else: + sys.argv.extend(argv) + + program_version = "v%s" % __version__ + program_build_date = str(__updated__) + program_version_message = '%%(prog)s %s (%s)' % (program_version, program_build_date) + program_short_description = "CTD2Galaxy - A project from the GenericWorkflowNodes family " \ + "(https://github.com/orgs/genericworkflownodes)" + program_usage = ''' + USAGE: + + I - Parsing a single CTD file and generate a Galaxy wrapper: + + $ python generator.py -i input.ctd -o output.xml + + + II - Parsing all found CTD files (files with .ctd and .xml extension) in a given folder and + output converted Galaxy wrappers in a given folder: + + $ python generator.py -i /home/user/*.ctd -o /home/user/galaxywrappers + + + III - Providing file formats, mimetypes + + Galaxy supports the concept of file format in order to connect compatible ports, that is, input ports of a certain + data format will be able to receive data from a port from the same format. This converter allows you to provide + a personalized file in which you can relate the CTD data formats with supported Galaxy data formats. The layout of + this file consists of lines, each of either one or four columns separated by any amount of whitespace. The content + of each column is as follows: + + * 1st column: file extension + * 2nd column: data type, as listed in Galaxy + * 3rd column: full-named Galaxy data type, as it will appear on datatypes_conf.xml + * 4th column: mimetype (optional) + + The following is an example of a valid "file formats" file: + + ########################################## FILE FORMATS example ########################################## + # Every line starting with a # will be handled as a comment and will not be parsed. + # The first column is the file format as given in the CTD and second column is the Galaxy data format. + # The second, third, fourth and fifth column can be left empty if the data type has already been registered + # in Galaxy, otherwise, all but the mimetype must be provided. + + # CTD type # Galaxy type # Long Galaxy data type # Mimetype + csv tabular galaxy.datatypes.data:Text + fasta + ini txt galaxy.datatypes.data:Text + txt + idxml txt galaxy.datatypes.xml:GenericXml application/xml + options txt galaxy.datatypes.data:Text + grid grid galaxy.datatypes.data:Grid + + ########################################################################################################## + + Note that each line consists precisely of either one, three or four columns. In the case of data types already + registered in Galaxy (such as fasta and txt in the above example), only the first column is needed. In the case of + data types that haven't been yet registered in Galaxy, the first three columns are needed (mimetype is optional). + + For information about Galaxy data types and subclasses, see the following page: + https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes + + + IV - Hardcoding parameters + + It is possible to hardcode parameters. This makes sense if you want to set a tool in Galaxy in 'quiet' mode or if + your tools support multi-threading and accept the number of threads via a parameter, without giving the end user the + chance to change the values for these parameters. + + In order to generate hardcoded parameters, you need to provide a simple file. Each line of this file contains two + or three columns separated by whitespace. Any line starting with a '#' will be ignored. The first column contains + the name of the parameter, the second column contains the value that will always be set for this parameter. The + first two columns are mandatory. + + If the parameter is to be hardcoded only for a set of tools, then a third column can be added. This column includes + a comma-separated list of tool names for which the parameter will be hardcoded. If a third column is not included, + then all processed tools containing the given parameter will get a hardcoded value for it. + + The following is an example of a valid file: + + ##################################### HARDCODED PARAMETERS example ##################################### + # Every line starting with a # will be handled as a comment and will not be parsed. + # The first column is the name of the parameter and the second column is the value that will be used. + + # Parameter name # Value # Tool(s) + threads \${GALAXY_SLOTS:-24} + mode quiet + xtandem_executable xtandem XTandemAdapter + verbosity high Foo, Bar + + ######################################################################################################### + + Using the above file will produce a similar to: + + [tool_name] ... -threads \${GALAXY_SLOTS:-24} -mode quiet ... + + For all tools. For XTandemAdapter, the will be similar to: + + XtandemAdapter ... -threads \${GALAXY_SLOTS:-24} -mode quiet -xtandem_executable xtandem ... + + And for tools Foo and Bar, the will be similar to: + + Foo ... ... -threads \${GALAXY_SLOTS:-24} -mode quiet -verbosity high ... + + + V - Control which tools will be converted + + Sometimes only a subset of CTDs needs to be converted. It is possible to either explicitly specify which tools will + be converted or which tools will not be converted. + + The value of the -s/--skip-tools parameter is a file in which each line will be interpreted as the name of a tool + that will not be converted. Conversely, the value of the -r/--required-tools is a file in which each line will be + interpreted as a tool that is required. Only one of these parameters can be specified at a given time. + + The format of both files is exactly the same. As stated before, each line will be interpreted as the name of a tool; + any line starting with a '#' will be ignored. + + ''' + program_license = '''%(short_description)s + Copyright 2015, Luis de la Garza + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + + %(usage)s +''' % {'short_description': program_short_description, 'usage': program_usage} + + try: + # Setup argument parser + parser = ArgumentParser(prog="CTD2Galaxy", description=program_license, + formatter_class=RawDescriptionHelpFormatter, add_help=True) + parser.add_argument("-i", "--input", dest="input_files", default=[], required=True, nargs="+", action="append", + help="List of CTD files to convert.") + parser.add_argument("-o", "--output-destination", dest="output_destination", required=True, + help="If multiple input files are given, then a folder in which all generated " + "XMLs will be generated is expected;" + "if a single input file is given, then a destination file is expected.") + parser.add_argument("-f", "--formats-file", dest="formats_file", + help="File containing the supported file formats. Run with '-h' or '--help' to see a " + "brief example on the layout of this file.", default=None, required=False) + parser.add_argument("-a", "--add-to-command-line", dest="add_to_command_line", + help="Adds content to the command line", default="", required=False) + parser.add_argument("-d", "--datatypes-destination", dest="data_types_destination", + help="Specify the location of a datatypes_conf.xml to modify and add the registered " + "data types. If the provided destination does not exist, a new file will be created.", + default=None, required=False) + parser.add_argument("-x", "--default-executable-path", dest="default_executable_path", + help="Use this executable path when is not present in the CTD", + default=None, required=False) + parser.add_argument("-b", "--blacklist-parameters", dest="blacklisted_parameters", default=[], nargs="+", action="append", + help="List of parameters that will be ignored and won't appear on the galaxy stub", + required=False) + parser.add_argument("-c", "--default-category", dest="default_category", default="DEFAULT", required=False, + help="Default category to use for tools lacking a category when generating tool_conf.xml") + parser.add_argument("-t", "--tool-conf-destination", dest="tool_conf_destination", default=None, required=False, + help="Specify the location of an existing tool_conf.xml that will be modified to include " + "the converted tools. If the provided destination does not exist, a new file will" + "be created.") + parser.add_argument("-g", "--galaxy-tool-path", dest="galaxy_tool_path", default=None, required=False, + help="The path that will be prepended to the file names when generating tool_conf.xml") + parser.add_argument("-r", "--required-tools", dest="required_tools_file", default=None, required=False, + help="Each line of the file will be interpreted as a tool name that needs translation. " + "Run with '-h' or '--help' to see a brief example on the format of this file.") + parser.add_argument("-s", "--skip-tools", dest="skip_tools_file", default=None, required=False, + help="File containing a list of tools for which a Galaxy stub will not be generated. " + "Run with '-h' or '--help' to see a brief example on the format of this file.") + parser.add_argument("-m", "--macros", dest="macros_files", default=[], nargs="*", + action="append", required=None, help="Import the additional given file(s) as macros. " + "The macros stdio, requirements and advanced_options are required. Please see " + "macros.xml for an example of a valid macros file. Al defined macros will be imported.") + parser.add_argument("-p", "--hardcoded-parameters", dest="hardcoded_parameters", default=None, required=False, + help="File containing hardcoded values for the given parameters. Run with '-h' or '--help' " + "to see a brief example on the format of this file.") + parser.add_argument("-v", "--validation-schema", dest="xsd_location", default=None, required=False, + help="Location of the schema to use to validate CTDs.") + + # TODO: add verbosity, maybe? + parser.add_argument("-V", "--version", action='version', version=program_version_message) + + # Process arguments + args = parser.parse_args() + + # validate and prepare the passed arguments + validate_and_prepare_args(args) + + # extract the names of the macros and check that we have found the ones we need + macros_to_expand = parse_macros_files(args.macros_files) + + # parse the given supported file-formats file + supported_file_formats = parse_file_formats(args.formats_file) + + # parse the hardcoded parameters file¬ + parameter_hardcoder = parse_hardcoded_parameters(args.hardcoded_parameters) + + # parse the skip/required tools files + skip_tools = parse_tools_list_file(args.skip_tools_file) + required_tools = parse_tools_list_file(args.required_tools_file) + + #if verbose > 0: + # print("Verbose mode on") + parsed_models = convert(args.input_files, + args.output_destination, + supported_file_formats=supported_file_formats, + default_executable_path=args.default_executable_path, + add_to_command_line=args.add_to_command_line, + blacklisted_parameters=args.blacklisted_parameters, + required_tools=required_tools, + skip_tools=skip_tools, + macros_file_names=args.macros_files, + macros_to_expand=macros_to_expand, + parameter_hardcoder=parameter_hardcoder, + xsd_location=args.xsd_location) + + #TODO: add some sort of warning if a macro that doesn't exist is to be expanded + + # it is not needed to copy the macros files, since the user has provided them + + # generation of galaxy stubs is ready... now, let's see if we need to generate a tool_conf.xml + if args.tool_conf_destination is not None: + generate_tool_conf(parsed_models, args.tool_conf_destination, + args.galaxy_tool_path, args.default_category) + + # now datatypes_conf.xml + if args.data_types_destination is not None: + generate_data_type_conf(supported_file_formats, args.data_types_destination) + + return 0 + + except KeyboardInterrupt: + # handle keyboard interrupt + return 0 + except ApplicationException, e: + error("CTD2Galaxy could not complete the requested operation.", 0) + error("Reason: " + e.msg, 0) + return 1 + except ModelError, e: + error("There seems to be a problem with one of your input CTDs.", 0) + error("Reason: " + e.msg, 0) + return 1 + except Exception, e: + traceback.print_exc() + return 2 + + +def parse_tools_list_file(tools_list_file): + tools_list = None + if tools_list_file is not None: + tools_list = [] + with open(tools_list_file) as f: + for line in f: + if line is None or not line.strip() or line.strip().startswith("#"): + continue + else: + tools_list.append(line.strip()) + + return tools_list + + +def parse_macros_files(macros_file_names): + macros_to_expand = set() + + for macros_file_name in macros_file_names: + try: + macros_file = open(macros_file_name) + info("Loading macros from %s" % macros_file_name, 0) + root = parse(macros_file).getroot() + for xml_element in root.findall("xml"): + name = xml_element.attrib["name"] + if name in macros_to_expand: + warning("Macro %s has already been found. Duplicate found in file %s." % + (name, macros_file_name), 0) + else: + info("Macro %s found" % name, 1) + macros_to_expand.add(name) + except ParseError, e: + raise ApplicationException("The macros file " + macros_file_name + " could not be parsed. Cause: " + + str(e)) + except IOError, e: + raise ApplicationException("The macros file " + macros_file_name + " could not be opened. Cause: " + + str(e)) + + # we depend on "stdio", "requirements" and "advanced_options" to exist on all the given macros files + missing_needed_macros = [] + for required_macro in REQUIRED_MACROS: + if required_macro not in macros_to_expand: + missing_needed_macros.append(required_macro) + + if missing_needed_macros: + raise ApplicationException( + "The following required macro(s) were not found in any of the given macros files: %s, " + "see sample_files/macros.xml for an example of a valid macros file." + % ", ".join(missing_needed_macros)) + + # we do not need to "expand" the advanced_options macro + macros_to_expand.remove(ADVANCED_OPTIONS_MACRO_NAME) + return macros_to_expand + + +def parse_hardcoded_parameters(hardcoded_parameters_file): + parameter_hardcoder = ParameterHardcoder() + if hardcoded_parameters_file is not None: + line_number = 0 + with open(hardcoded_parameters_file) as f: + for line in f: + line_number += 1 + if line is None or not line.strip() or line.strip().startswith("#"): + pass + else: + # the third column must not be obtained as a whole, and not split + parsed_hardcoded_parameter = line.strip().split(None, 2) + # valid lines contain two or three columns + if len(parsed_hardcoded_parameter) != 2 and len(parsed_hardcoded_parameter) != 3: + warning("Invalid line at line number %d of the given hardcoded parameters file. Line will be" + "ignored:\n%s" % (line_number, line), 0) + continue + + parameter_name = parsed_hardcoded_parameter[0] + hardcoded_value = parsed_hardcoded_parameter[1] + tool_names = None + if len(parsed_hardcoded_parameter) == 3: + tool_names = parsed_hardcoded_parameter[2].split(',') + if tool_names: + for tool_name in tool_names: + parameter_hardcoder.register_parameter(parameter_name, hardcoded_value, tool_name.strip()) + else: + parameter_hardcoder.register_parameter(parameter_name, hardcoded_value) + + return parameter_hardcoder + + +def parse_file_formats(formats_file): + supported_formats = {} + if formats_file is not None: + line_number = 0 + with open(formats_file) as f: + for line in f: + line_number += 1 + if line is None or not line.strip() or line.strip().startswith("#"): + # ignore (it'd be weird to have something like: + # if line is not None and not (not line.strip()) ... + pass + else: + # not an empty line, no comment + # strip the line and split by whitespace + parsed_formats = line.strip().split() + # valid lines contain either one or four columns + if not (len(parsed_formats) == 1 or len(parsed_formats) == 3 or len(parsed_formats) == 4): + warning("Invalid line at line number %d of the given formats file. Line will be ignored:\n%s" % + (line_number, line), 0) + # ignore the line + continue + elif len(parsed_formats) == 1: + supported_formats[parsed_formats[0]] = DataType(parsed_formats[0], parsed_formats[0]) + else: + mimetype = None + # check if mimetype was provided + if len(parsed_formats) == 4: + mimetype = parsed_formats[3] + supported_formats[parsed_formats[0]] = DataType(parsed_formats[0], parsed_formats[1], + parsed_formats[2], mimetype) + return supported_formats + + +def validate_and_prepare_args(args): + # check that only one of skip_tools_file and required_tools_file has been provided + if args.skip_tools_file is not None and args.required_tools_file is not None: + raise ApplicationException( + "You have provided both a file with tools to ignore and a file with required tools.\n" + "Only one of -s/--skip-tools, -r/--required-tools can be provided.") + + # first, we convert all list of lists in args to flat lists + lists_to_flatten = ["input_files", "blacklisted_parameters", "macros_files"] + for list_to_flatten in lists_to_flatten: + setattr(args, list_to_flatten, [item for sub_list in getattr(args, list_to_flatten) for item in sub_list]) + + # if input is a single file, we expect output to be a file (and not a dir that already exists) + if len(args.input_files) == 1: + if os.path.isdir(args.output_destination): + raise ApplicationException("If a single input file is provided, output (%s) is expected to be a file " + "and not a folder.\n" % args.output_destination) + + # if input is a list of files, we expect output to be a folder + if len(args.input_files) > 1: + if not os.path.isdir(args.output_destination): + raise ApplicationException("If several input files are provided, output (%s) is expected to be an " + "existing directory.\n" % args.output_destination) + + # check that the provided input files, if provided, contain a valid file path + input_variables_to_check = ["skip_tools_file", "required_tools_file", "macros_files", "xsd_location", + "input_files", "formats_file", "hardcoded_parameters"] + + for variable_name in input_variables_to_check: + paths_to_check = [] + # check if we are handling a single file or a list of files + member_value = getattr(args, variable_name) + if member_value is not None: + if isinstance(member_value, list): + for file_name in member_value: + paths_to_check.append(strip(str(file_name))) + else: + paths_to_check.append(strip(str(member_value))) + + for path_to_check in paths_to_check: + if not os.path.isfile(path_to_check) or not os.path.exists(path_to_check): + raise ApplicationException( + "The provided input file (%s) does not exist or is not a valid file path." + % path_to_check) + + # check that the provided output files, if provided, contain a valid file path (i.e., not a folder) + output_variables_to_check = ["data_types_destination", "tool_conf_destination"] + + for variable_name in output_variables_to_check: + file_name = getattr(args, variable_name) + if file_name is not None and os.path.isdir(file_name): + raise ApplicationException("The provided output file name (%s) points to a directory." % file_name) + + if not args.macros_files: + # list is empty, provide the default value + warning("Using default macros from macros.xml", 0) + args.macros_files = ["macros.xml"] + + +def convert(input_files, output_destination, **kwargs): + # first, generate a model + is_converting_multiple_ctds = len(input_files) > 1 + parsed_models = [] + schema = None + if kwargs["xsd_location"] is not None: + try: + info("Loading validation schema from %s" % kwargs["xsd_location"], 0) + schema = etree.XMLSchema(etree.parse(kwargs["xsd_location"])) + except Exception, e: + error("Could not load validation schema %s. Reason: %s" % (kwargs["xsd_location"], str(e)), 0) + else: + info("Validation against a schema has not been enabled.", 0) + for input_file in input_files: + try: + if schema is not None: + validate_against_schema(input_file, schema) + model = CTDModel(from_file=input_file) + except Exception, e: + error(str(e), 1) + continue + + if kwargs["skip_tools"] is not None and model.name in kwargs["skip_tools"]: + info("Skipping tool %s" % model.name, 0) + continue + elif kwargs["required_tools"] is not None and model.name not in kwargs["required_tools"]: + info("Tool %s is not required, skipping it" % model.name, 0) + continue + else: + info("Converting from %s " % input_file, 0) + tool = create_tool(model) + write_header(tool, model) + create_description(tool, model) + expand_macros(tool, model, **kwargs) + create_command(tool, model, **kwargs) + create_inputs(tool, model, **kwargs) + create_outputs(tool, model, **kwargs) + create_help(tool, model) + + # finally, serialize the tool + output_file = output_destination + # if multiple inputs are being converted, + # then we need to generate a different output_file for each input + if is_converting_multiple_ctds: + output_file = os.path.join(output_file, get_filename_without_suffix(input_file) + ".xml") + # wrap our tool element into a tree to be able to serialize it + tree = ElementTree(tool) + tree.write(open(output_file, 'w'), encoding="UTF-8", xml_declaration=True, pretty_print=True) + # let's use model to hold the name of the output file + parsed_models.append([model, get_filename(output_file)]) + + return parsed_models + + +# validates a ctd file against the schema +def validate_against_schema(ctd_file, schema): + try: + parser = etree.XMLParser(schema=schema) + etree.parse(ctd_file, parser=parser) + except etree.XMLSyntaxError, e: + raise ApplicationException("Input ctd file %s is not valid. Reason: %s" % (ctd_file, str(e))) + + +def write_header(tool, model): + tool.addprevious(etree.Comment( + "This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). " + "This file was automatically generated using CTD2Galaxy.")) + tool.addprevious(etree.Comment('Proposed Tool Section: [%s]' % model.opt_attribs.get("category", ""))) + + +def generate_tool_conf(parsed_models, tool_conf_destination, galaxy_tool_path, default_category): + # for each category, we keep a list of models corresponding to it + categories_to_tools = dict() + for model in parsed_models: + category = strip(model[0].opt_attribs.get("category", "")) + if not category.strip(): + category = default_category + if category not in categories_to_tools: + categories_to_tools[category] = [] + categories_to_tools[category].append(model[1]) + + # at this point, we should have a map for all categories->tools + toolbox_node = Element("toolbox") + + if galaxy_tool_path is not None and not galaxy_tool_path.strip().endswith("/"): + galaxy_tool_path = galaxy_tool_path.strip() + "/" + if galaxy_tool_path is None: + galaxy_tool_path = "" + + for category, file_names in categories_to_tools.iteritems(): + section_node = add_child_node(toolbox_node, "section") + section_node.attrib["id"] = "section-id-" + "".join(category.split()) + section_node.attrib["name"] = category + + for filename in file_names: + tool_node = add_child_node(section_node, "tool") + tool_node.attrib["file"] = galaxy_tool_path + filename + + toolconf_tree = ElementTree(toolbox_node) + toolconf_tree.write(open(tool_conf_destination,'w'), encoding="UTF-8", xml_declaration=True, pretty_print=True) + info("Generated Galaxy tool_conf.xml in %s" % tool_conf_destination, 0) + + +def generate_data_type_conf(supported_file_formats, data_types_destination): + data_types_node = Element("datatypes") + registration_node = add_child_node(data_types_node, "registration") + registration_node.attrib["converters_path"] = "lib/galaxy/datatypes/converters" + registration_node.attrib["display_path"] = "display_applications" + + for format_name in supported_file_formats: + data_type = supported_file_formats[format_name] + # add only if it's a data type that does not exist in Galaxy + if data_type.galaxy_type is not None: + data_type_node = add_child_node(registration_node, "datatype") + # we know galaxy_extension is not None + data_type_node.attrib["extension"] = data_type.galaxy_extension + data_type_node.attrib["type"] = data_type.galaxy_type + if data_type.mimetype is not None: + data_type_node.attrib["mimetype"] = data_type.mimetype + + data_types_tree = ElementTree(data_types_node) + data_types_tree.write(open(data_types_destination,'w'), encoding="UTF-8", xml_declaration=True, pretty_print=True) + info("Generated Galaxy datatypes_conf.xml in %s" % data_types_destination, 0) + + +# taken from +# http://stackoverflow.com/questions/8384737/python-extract-file-name-from-path-no-matter-what-the-os-path-format +def get_filename(path): + head, tail = ntpath.split(path) + return tail or ntpath.basename(head) + + +def get_filename_without_suffix(path): + root, ext = os.path.splitext(os.path.basename(path)) + return root + + +def create_tool(model): + return Element("tool", OrderedDict([("id", model.name), ("name", model.name), ("version", model.version)])) + + +def create_description(tool, model): + if "description" in model.opt_attribs.keys() and model.opt_attribs["description"] is not None: + description = SubElement(tool,"description") + description.text = model.opt_attribs["description"] + + +def get_param_cli_name(param, model): + # we generate parameters with colons for subgroups, but not for the two topmost parents (OpenMS legacy) + if type(param.parent) == ParameterGroup: + if not hasattr(param.parent.parent, 'parent'): + return resolve_param_mapping(param, model) + elif not hasattr(param.parent.parent.parent, 'parent'): + return resolve_param_mapping(param, model) + else: + if model.cli: + warning("Using nested parameter sections (NODE elements) is not compatible with ", py1) + return get_param_name(param.parent) + ":" + resolve_param_mapping(param, model) + else: + return resolve_param_mapping(param, model) + + +def get_param_name(param): + # we generate parameters with colons for subgroups, but not for the two topmost parents (OpenMS legacy) + if type(param.parent) == ParameterGroup: + if not hasattr(param.parent.parent, 'parent'): + return param.name + elif not hasattr(param.parent.parent.parent, 'parent'): + return param.name + else: + return get_param_name(param.parent) + ":" + param.name + else: + return param.name + + +# some parameters are mapped to command line options, this method helps resolve those mappings, if any +def resolve_param_mapping(param, model): + # go through all mappings and find if the given param appears as a reference name in a mapping element + param_mapping = None + for cli_element in model.cli: + for mapping_element in cli_element.mappings: + if mapping_element.reference_name == param.name: + if param_mapping is not None: + warning("The parameter %s has more than one mapping in the section. " + "The first found mapping, %s, will be used." % (param.name, param_mapping), 1) + else: + param_mapping = cli_element.option_identifier + + return param_mapping if param_mapping is not None else param.name + +def create_command(tool, model, **kwargs): + final_command = get_tool_executable_path(model, kwargs["default_executable_path"]) + '\n' + final_command += kwargs["add_to_command_line"] + '\n' + advanced_command_start = "#if $adv_opts.adv_opts_selector=='advanced':\n" + advanced_command_end = '#end if' + advanced_command = '' + parameter_hardcoder = kwargs["parameter_hardcoder"] + + found_output_parameter = False + for param in extract_parameters(model): + if param.type is _OutFile: + found_output_parameter = True + command = '' + param_name = get_param_name(param) + param_cli_name = get_param_cli_name(param, model) + if param_name == param_cli_name: + # there was no mapping, so for the cli name we will use a '-' in the prefix + param_cli_name = '-' + param_name + + if param.name in kwargs["blacklisted_parameters"]: + continue + + hardcoded_value = parameter_hardcoder.get_hardcoded_value(param_name, model.name) + if hardcoded_value: + command += '%s %s\n' % (param_cli_name, hardcoded_value) + else: + # parameter is neither blacklisted nor hardcoded... + galaxy_parameter_name = get_galaxy_parameter_name(param) + repeat_galaxy_parameter_name = get_repeat_galaxy_parameter_name(param) + + # logic for ITEMLISTs + if param.is_list: + if param.type is _InFile: + command += param_cli_name + "\n" + command += " #for token in $" + galaxy_parameter_name + ":\n" + command += " $token\n" + command += " #end for\n" + else: + command += "\n#if $" + repeat_galaxy_parameter_name + ":\n" + command += param_cli_name + "\n" + command += " #for token in $" + repeat_galaxy_parameter_name + ":\n" + command += " #if \" \" in str(token):\n" + command += " \"$token." + galaxy_parameter_name + "\"\n" + command += " #else\n" + command += " $token." + galaxy_parameter_name + "\n" + command += " #end if\n" + command += " #end for\n" + command += "#end if\n" + # logic for other ITEMs + else: + if param.advanced and param.type is not _OutFile: + actual_parameter = "$adv_opts.%s" % galaxy_parameter_name + else: + actual_parameter = "$%s" % galaxy_parameter_name + ## if whitespace_validation has been set, we need to generate, for each parameter: + ## #if str( $t ).split() != '': + ## -t "$t" + ## #end if + ## TODO only useful for text fields, integers or floats + ## not useful for choices, input fields ... + + if not is_boolean_parameter(param) and type(param.restrictions) is _Choices : + command += "#if " + actual_parameter + ":\n" + command += ' %s\n' % param_cli_name + command += " #if \" \" in str(" + actual_parameter + "):\n" + command += " \"" + actual_parameter + "\"\n" + command += " #else\n" + command += " " + actual_parameter + "\n" + command += " #end if\n" + command += "#end if\n" + elif is_boolean_parameter(param): + command += "#if " + actual_parameter + ":\n" + command += ' %s\n' % param_cli_name + command += "#end if\n" + elif TYPE_TO_GALAXY_TYPE[param.type] is 'text': + command += "#if " + actual_parameter + ":\n" + command += " %s " % param_cli_name + command += " \"" + actual_parameter + "\"\n" + command += "#end if\n" + else: + command += "#if " + actual_parameter + ":\n" + command += ' %s ' % param_cli_name + command += actual_parameter + "\n" + command += "#end if\n" + + if param.advanced and param.type is not _OutFile: + advanced_command += " %s" % command + else: + final_command += command + + if advanced_command: + final_command += "%s%s%s\n" % (advanced_command_start, advanced_command, advanced_command_end) + + if not found_output_parameter: + final_command += "> $param_stdout\n" + + command_node = add_child_node(tool, "command") + command_node.text = final_command + + +# creates the xml elements needed to import the needed macros files +# and to "expand" the macros +def expand_macros(tool, model, **kwargs): + macros_node = add_child_node(tool, "macros") + token_node = add_child_node(macros_node, "token") + token_node.attrib["name"] = "@EXECUTABLE@" + token_node.text = get_tool_executable_path(model, kwargs["default_executable_path"]) + + # add nodes + for macro_file_name in kwargs["macros_file_names"]: + macro_file = open(macro_file_name) + import_node = add_child_node(macros_node, "import") + # do not add the path of the file, rather, just its basename + import_node.text = os.path.basename(macro_file.name) + + # add nodes + for expand_macro in kwargs["macros_to_expand"]: + expand_node = add_child_node(tool, "expand") + expand_node.attrib["macro"] = expand_macro + + +def get_tool_executable_path(model, default_executable_path): + # rules to build the galaxy executable path: + # if executablePath is null, then use default_executable_path and store it in executablePath + # if executablePath is null and executableName is null, then the name of the tool will be used + # if executablePath is null and executableName is not null, then executableName will be used + # if executablePath is not null and executableName is null, + # then executablePath and the name of the tool will be used + # if executablePath is not null and executableName is not null, then both will be used + + # first, check if the model has executablePath / executableName defined + executable_path = model.opt_attribs.get("executablePath", None) + executable_name = model.opt_attribs.get("executableName", None) + + # check if we need to use the default_executable_path + if executable_path is None: + executable_path = default_executable_path + + # fix the executablePath to make sure that there is a '/' in the end + if executable_path is not None: + executable_path = executable_path.strip() + if not executable_path.endswith('/'): + executable_path += '/' + + # assume that we have all information present + command = str(executable_path) + str(executable_name) + if executable_path is None: + if executable_name is None: + command = model.name + else: + command = executable_name + else: + if executable_name is None: + command = executable_path + model.name + return command + + +def get_galaxy_parameter_name(param): + return "param_%s" % get_param_name(param).replace(':', '_').replace('-', '_') + + +def get_input_with_same_restrictions(out_param, model, supported_file_formats): + for param in extract_parameters(model): + if param.type is _InFile: + if param.restrictions is not None: + in_param_formats = get_supported_file_types(param.restrictions.formats, supported_file_formats) + out_param_formats = get_supported_file_types(out_param.restrictions.formats, supported_file_formats) + if in_param_formats == out_param_formats: + return param + + +def create_inputs(tool, model, **kwargs): + inputs_node = SubElement(tool, "inputs") + + # some suites (such as OpenMS) need some advanced options when handling inputs + expand_advanced_node = add_child_node(tool, "expand", OrderedDict([("macro", ADVANCED_OPTIONS_MACRO_NAME)])) + parameter_hardcoder = kwargs["parameter_hardcoder"] + + # treat all non output-file parameters as inputs + for param in extract_parameters(model): + # no need to show hardcoded parameters + hardcoded_value = parameter_hardcoder.get_hardcoded_value(param.name, model.name) + if param.name in kwargs["blacklisted_parameters"] or hardcoded_value: + # let's not use an extra level of indentation and use NOP + continue + if param.type is not _OutFile: + if param.advanced: + if expand_advanced_node is not None: + parent_node = expand_advanced_node + else: + # something went wrong... we are handling an advanced parameter and the + # advanced input macro was not set... inform the user about it + info("The parameter %s has been set as advanced, but advanced_input_macro has " + "not been set." % param.name, 1) + # there is not much we can do, other than use the inputs_node as a parent node! + parent_node = inputs_node + else: + parent_node = inputs_node + + # for lists we need a repeat tag + if param.is_list and param.type is not _InFile: + rep_node = add_child_node(parent_node, "repeat") + create_repeat_attribute_list(rep_node, param) + parent_node = rep_node + + param_node = add_child_node(parent_node, "param") + create_param_attribute_list(param_node, param, kwargs["supported_file_formats"]) + + # advanced parameter selection should be at the end + # and only available if an advanced parameter exists + if expand_advanced_node is not None and len(expand_advanced_node) > 0: + inputs_node.append(expand_advanced_node) + + +def get_repeat_galaxy_parameter_name(param): + return "rep_" + get_galaxy_parameter_name(param) + + +def create_repeat_attribute_list(rep_node, param): + rep_node.attrib["name"] = get_repeat_galaxy_parameter_name(param) + if param.required: + rep_node.attrib["min"] = "1" + else: + rep_node.attrib["min"] = "0" + # for the ITEMLISTs which have LISTITEM children we only + # need one parameter as it is given as a string + if param.default is not None: + rep_node.attrib["max"] = "1" + rep_node.attrib["title"] = get_galaxy_parameter_name(param) + + +def create_param_attribute_list(param_node, param, supported_file_formats): + param_node.attrib["name"] = get_galaxy_parameter_name(param) + + param_type = TYPE_TO_GALAXY_TYPE[param.type] + if param_type is None: + raise ModelError("Unrecognized parameter type %(type)s for parameter %(name)s" + % {"type": param.type, "name": param.name}) + + if param.is_list: + param_type = "text" + + if is_selection_parameter(param): + param_type = "select" + if len(param.restrictions.choices) < 5: + param_node.attrib["display"] = "radio" + + if is_boolean_parameter(param): + param_type = "boolean" + + if param.type is _InFile: + # assume it's just text unless restrictions are provided + param_format = "text" + if param.restrictions is not None: + # join all formats of the file, take mapping from supported_file if available for an entry + if type(param.restrictions) is _FileFormat: + param_format = ','.join([get_supported_file_type(i, supported_file_formats) if + get_supported_file_type(i, supported_file_formats) + else i for i in param.restrictions.formats]) + else: + raise InvalidModelException("Expected 'file type' restrictions for input file [%(name)s], " + "but instead got [%(type)s]" + % {"name": param.name, "type": type(param.restrictions)}) + + param_node.attrib["type"] = "data" + param_node.attrib["format"] = param_format + # in the case of multiple input set multiple flag + if param.is_list: + param_node.attrib["multiple"] = "true" + + else: + param_node.attrib["type"] = param_type + + # check for parameters with restricted values (which will correspond to a "select" in galaxy) + if param.restrictions is not None: + # it could be either _Choices or _NumericRange, with special case for boolean types + if param_type == "boolean": + create_boolean_parameter(param_node, param) + elif type(param.restrictions) is _Choices: + # create as many