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comparison tandem_to_pepxml.xml @ 14:9d6e0ad4d600 draft

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Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 19:53:53 -0400
parents ffd1d25b8080
children 0faaab4f192a
comparison
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13:c60d1f18fd85 14:9d6e0ad4d600
1 <tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.0.1"> 1 <tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.0">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="1.3.0">protk</requirement> 3 <container type="docker">iracooke/protk-1.4.1</container>
4 <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> 4 <requirement type="package" version="1.4">protk</requirement>
5 </requirements> 5 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
6 </requirements>
6 7
7 <description>Converts a tandem result file to pepXML</description> 8 <description>Converts a tandem result file to pepXML</description>
8 9
9 <command> 10 <command>
10 tandem_to_pepxml.rb $input_file -o $output 11 tandem_to_pepxml.rb $input_file -o $output
11 </command> 12 </command>
12 13
13 <inputs> 14 <inputs>
14 <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/> 15 <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/>
15 </inputs> 16 </inputs>
16 17
17 <outputs> 18 <outputs>
18 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" /> 19 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
19 </outputs> 20 </outputs>
20 21
21 <help> 22 <help>
22 Convert X!Tandem results to pepXML 23 Convert X!Tandem results to pepXML
23 </help> 24 </help>
25
26 <tests>
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>
24 37
25 </tool> 38 </tool>