Mercurial > repos > iracooke > tpp_prophets

comparison protxml_to_table.xml @ 18:84b47300a4c8 draft default tip

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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 20:46:16 -0400
parents b68f292b2904
children
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17:b68f292b2904 18:84b47300a4c8
1 <tool id="protxml_to_table_1" name="ProtXML to Table" version="1.0.1"> 1 <tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.1">
2 <requirements> 2 <description>Converts a ProtXML file to a table</description>
3 <container type="docker">simonalpha/protk:1.4.0</container> 3 <requirements>
4 <requirement type="package" version="1.3">protk</requirement> 4 <container type="docker">iracooke/protk-1.4.3</container>
5 </requirements> 5 <requirement type="package" version="1.4.3">protk</requirement>
6 6 </requirements>
7 <description>Converts a ProtXML file to a table</description> 7 <command>
8 8 protxml_to_table.rb
9 <command> 9 $invert_probs
10 protxml_to_table.rb 10 $input_file
11 $invert_probs 11 -o $output
12 12 </command>
13 $input_file 13 <inputs>
14 -o $output 14 <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/>
15 </command> 15 <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
16 16 </inputs>
17 <inputs> 17 <outputs>
18 18 <data format="tabular" name="output" />
19 <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/> 19 </outputs>
20 <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> 20 <tests>
21 </inputs> 21 <!-- Just test that the tool runs and produces vaguely correct output -->
22 22 <test>
23 23 <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml" format="protxml"/>
24 <outputs> 24 <output name="output" format="tabular">
25 <data format="tabular" name="output" /> 25 <assert_contents>
26 </outputs> 26 <has_text text="AVQKYLTAHEQSK" />
27 27 </assert_contents>
28 28 </output>
29 <help> 29 </test>
30 30 </tests>
31 <help>
31 **What it does** 32 **What it does**
32 33
33 Converts a ProtXML file to a tab separated table 34 Converts a ProtXML file to a tab separated table
34 35
35 </help> 36 </help>
36
37 </tool> 37 </tool>