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