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1 <tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.0">
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2 <requirements>
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3 <container type="docker">iracooke/protk-1.4.1</container>
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4 <requirement type="package" version="1.4">protk</requirement>
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5 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
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6 </requirements>
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7
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8 <description>Converts a tandem result file to pepXML</description>
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9
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10 <command>
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11 tandem_to_pepxml.rb $input_file -o $output
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12 </command>
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13
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14 <inputs>
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15 <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/>
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16 </inputs>
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17
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18 <outputs>
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19 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
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20 </outputs>
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21
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22 <help>
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23 Convert X!Tandem results to pepXML
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24 </help>
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25
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26 <tests>
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27 <!-- Just test that the tool runs and produces vaguely correct output -->
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28 <test>
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29 <param name="input_file" value="tandem_to_pepxml_test.tandem" format="tandem"/>
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30 <output name="output" format="raw_pepxml">
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31 <assert_contents>
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32 <has_text text="SQVFQLESTFDV" />
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33 </assert_contents>
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34 </output>
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35 </test>
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36 </tests>
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37
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38 </tool>
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