Mercurial > repos > iracooke > tpp_prophets

comparison pepxml_to_table.xml @ 15:0746a2ae9e04 draft

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:45:24 -0400
parents d90c8bc10a9c
children 1b86e378de37
comparison
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14:d90c8bc10a9c 15:0746a2ae9e04
1 <tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.0"> 1 <tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.1">
2 2 <description>Converts a pepXML file to a tab delimited text file</description>
3 <requirements> 3 <requirements>
4 <container type="docker">iracooke/protk-1.4.1</container> 4 <container type="docker">iracooke/protk-1.4.3</container>
5 <requirement type="package" version="1.4">protk</requirement> 5 <requirement type="package" version="1.4.3">protk</requirement>
6 </requirements> 6 </requirements>
7 7 <!-- Note .. the input file is assumed to be the first argument -->
8 8 <command>pepxml_to_table.rb $input_file -o $output $invert_probs</command>
9 9 <inputs>
10 <description>Converts a pepXML file to a tab delimited text file</description> 10 <param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Input File" help="A pepXML file"/>
11 11 <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
12 12 </inputs>
13 <!-- Note .. the input file is assumed to be the first argument --> 13 <outputs>
14 <command>pepxml_to_table.rb $input_file -o $output $invert_probs</command> 14 <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" />
15 15 </outputs>
16 16 <tests>
17 <inputs> 17 <!-- Just test that the tool runs and produces vaguely correct output -->
18 18 <test>
19 <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" value="mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" format="raw_pepxml"/>
20 <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> 20 <output name="output" format="csv">
21 21 <assert_contents>
22 </inputs> 22 <has_text text="ANTNNYAPKSSR" />
23 <outputs> 23 </assert_contents>
24 <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" /> 24 </output>
25 </outputs> 25 </test>
26 26 </tests>
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
41 <help> 27 <help>
42 Convert a pepXML file to Tab delimited text 28 Convert a pepXML file to Tab delimited text
43 </help> 29 </help>
44
45 </tool> 30 </tool>