| 7 | 7 |
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| 8 | 8 |
### Macros
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| 9 | 9 |
|
| 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.
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|
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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| 11 | 11 |
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| 12 | 12 |
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!
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| 13 | 13 |
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| 14 | 14 |
### One input, one Output
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| 15 | 15 |
|
| 16 | |
In its simplest form, `CTD2Galaxy` takes an input CTD file and generates an output Galaxy *ToolConfig* file. The following use of `CTD2Galaxy`:
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|
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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| 17 | 17 |
|
| 18 | 18 |
$ python generator.py -i /data/sample_input.ctd -o /data/sample_output.xml
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| 19 | 19 |
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|
| 154 | 154 |
|
| 155 | 155 |
### Generating a tool_conf.xml file
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| 156 | 156 |
|
| 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.
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|
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.
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| 158 | 158 |
* Short/long version: `-t` / `--tool-conf-destination`
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| 159 | 159 |
* Required: no.
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| 160 | 160 |
* Taken values: The destination of the file.
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|
| 331 | 331 |
* MapAlignerRTTransformer
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| 332 | 332 |
|
| 333 | 333 |
[CTDopts]: https://github.com/genericworkflownodes/CTDopts
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| 334 | |
[macros.xml]: https://github.com/WorkflowConversion/CTD2Galaxy/blob/master/macros.xml
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|
334 |
[macros.xml]: https://github.com/WorkflowConversion/CTDConverter/blob/master/galaxy/macros.xml
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| 335 | 335 |
[CTDSchema]: https://github.com/genericworkflownodes/CTDSchema⏎
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