Mercurial > repos > iracooke > xtandem

comparison tandem_to_pepxml.xml @ 15:0faaab4f192a draft

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:47:05 -0400
parents 9d6e0ad4d600
children 29e2df3edf11
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14:9d6e0ad4d600 15:0faaab4f192a
1 <tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.0"> 1 <tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.1">
2 <requirements> 2 <description>Converts a tandem result file to pepXML</description>
3 <container type="docker">iracooke/protk-1.4.1</container> 3 <requirements>
4 <requirement type="package" version="1.4">protk</requirement> 4 <container type="docker">iracooke/protk-1.4.3</container>
5 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> 5 <requirement type="package" version="1.4.3">protk</requirement>
6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
6 </requirements> 7 </requirements>
8 <command>
9 tandem_to_pepxml.rb $input_file -o $output
10 </command>
7 11
8 <description>Converts a tandem result file to pepXML</description> 12 <inputs>
13 <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/>
14 </inputs>
9 15
10 <command> 16 <outputs>
11 tandem_to_pepxml.rb $input_file -o $output 17 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
12 </command> 18 </outputs>
13 19 <tests>
14 <inputs> 20 <!-- Just test that the tool runs and produces vaguely correct output -->
15 <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/> 21 <test>
16 </inputs> 22 <param name="input_file" value="tandem_to_pepxml_test.tandem" format="tandem"/>
17 23 <output name="output" format="raw_pepxml">
18 <outputs> 24 <assert_contents>
19 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" /> 25 <has_text text="SQVFQLESTFDV" />
20 </outputs> 26 </assert_contents>
21 27 </output>
22 <help> 28 </test>
23 Convert X!Tandem results to pepXML 29 </tests>
24 </help> 30 <help>
25 31 Convert X!Tandem results to pepXML
26 <tests> 32 </help>
27 <!-- Just test that the tool runs and produces vaguely correct output -->
28 <test>
29 <param name="input_file" value="tandem_to_pepxml_test.tandem" format="tandem"/>
30 <output name="output" format="raw_pepxml">
31 <assert_contents>
32 <has_text text="SQVFQLESTFDV" />
33 </assert_contents>
34 </output>
35 </test>
36 </tests>
37
38 </tool> 33 </tool>