Mercurial > repos > iracooke > tpp_prophets

comparison pepxml_to_table.xml @ 14:d90c8bc10a9c draft

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Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 19:55:19 -0400
parents 4c66453a168e
children 0746a2ae9e04
comparison
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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>