Package list ctdconverter / 1f0b7ee
Got rid of mentions of the now unexistent CTD2Galaxy Luis de la Garza 4 years ago
2 changed file(s) with 4 addition(s) and 6 deletion(s). Raw diff Collapse all Expand all
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3636 [CTDopts]: https://github.com/genericworkflownodes/CTDopts
37 [macros.xml]: https://github.com/WorkflowConversion/CTD2Galaxy/blob/master/macros.xml
38 [CTDSchema]: https://github.com/genericworkflownodes/CTDSchema
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88 ### Macros
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10 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.
10 Galaxy supports the use of macros via a `macros.xml` file (we provide 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.
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1212 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!
1313
1414 ### One input, one Output
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16 In its simplest form, `CTD2Galaxy` takes an input CTD file and generates an output Galaxy *ToolConfig* file. The following use of `CTD2Galaxy`:
16 In its simplest form, the converter takes an input CTD file and generates an output Galaxy *ToolConfig* file. The following usage of `generator.py`:
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1818 $ python generator.py -i /data/sample_input.ctd -o /data/sample_output.xml
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154154
155155 ### Generating a tool_conf.xml file
156156
157 * 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 `<section>` will be generated. Any input CTD lacking a category will be sorted under the provided default category.
157 * Purpose: Galaxy uses a file `tool_conf.xml` in which other tools can be included. `generator.py` can also generate this file. Categories will be extracted from the provided input CTDs and for each category, a different `<section>` will be generated. Any input CTD lacking a category will be sorted under the provided default category.
158158 * Short/long version: `-t` / `--tool-conf-destination`
159159 * Required: no.
160160 * Taken values: The destination of the file.
331331 * MapAlignerRTTransformer
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333333 [CTDopts]: https://github.com/genericworkflownodes/CTDopts
334 [macros.xml]: https://github.com/WorkflowConversion/CTD2Galaxy/blob/master/macros.xml
334 [macros.xml]: https://github.com/WorkflowConversion/CTDConverter/blob/master/galaxy/macros.xml
335335 [CTDSchema]: https://github.com/genericworkflownodes/CTDSchema