Mercurial > repos > iracooke > tpp_prophets
comparison pepxml_to_table.xml @ 14:d90c8bc10a9c draft
Docker support and update for protk 1.4
| author | iracooke |
|---|---|
| date | Thu, 26 Mar 2015 19:55:19 -0400 |
| parents | 4c66453a168e |
| children | 0746a2ae9e04 |
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| 13:b793fe628648 | 14:d90c8bc10a9c |
|---|---|
| 1 <tool id="pepxml_to_table_1" name="PepXML to Table" version="1.0.1"> | 1 <tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.0"> |
| 2 | 2 |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.3">protk</requirement> | 4 <container type="docker">iracooke/protk-1.4.1</container> |
| 5 <requirement type="package" version="1.4">protk</requirement> | |
| 5 </requirements> | 6 </requirements> |
| 6 | 7 |
| 7 | 8 |
| 8 | 9 |
| 9 <description>Converts a pepXML file to a tab delimited text file</description> | 10 <description>Converts a pepXML file to a tab delimited text file</description> |
| 10 | 11 |
| 11 | 12 |
| 12 <!-- Note .. the input file is assumed to be the first argument --> | 13 <!-- Note .. the input file is assumed to be the first argument --> |
| 13 <command>pepxml_to_table.rb $input_file -o $output</command> | 14 <command>pepxml_to_table.rb $input_file -o $output $invert_probs</command> |
| 14 | 15 |
| 15 | 16 |
| 16 <inputs> | 17 <inputs> |
| 17 | 18 |
| 18 <param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Input File" help="A pepXML file"/> | 19 <param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Input File" help="A pepXML file"/> |
| 20 <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> | |
| 19 | 21 |
| 20 </inputs> | 22 </inputs> |
| 21 <outputs> | 23 <outputs> |
| 22 <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" /> | 24 <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" /> |
| 23 </outputs> | 25 </outputs> |
| 24 | 26 |
| 27 | |
| 28 <tests> | |
| 29 <!-- Just test that the tool runs and produces vaguely correct output --> | |
| 30 <test> | |
| 31 <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" format="raw_pepxml"/> | |
| 32 <output name="output" format="csv"> | |
| 33 <assert_contents> | |
| 34 <has_text text="ANTNNYAPKSSR" /> | |
| 35 </assert_contents> | |
| 36 </output> | |
| 37 </test> | |
| 38 </tests> | |
| 39 | |
| 40 | |
| 25 <help> | 41 <help> |
| 26 Convert a pepXML file to Tab delimited text | 42 Convert a pepXML file to Tab delimited text |
| 27 </help> | 43 </help> |
| 28 | 44 |
| 29 </tool> | 45 </tool> |