14
|
1 <tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.0">
|
12
|
2 <requirements>
|
14
|
3 <container type="docker">iracooke/protk-1.4.1</container>
|
|
4 <requirement type="package" version="1.4">protk</requirement>
|
12
|
5 </requirements>
|
|
6
|
|
7 <description>Converts a ProtXML file to a table</description>
|
|
8
|
|
9 <command>
|
|
10 protxml_to_table.rb
|
14
|
11 $invert_probs
|
12
|
12
|
|
13 $input_file
|
|
14 -o $output
|
|
15 </command>
|
|
16
|
|
17 <inputs>
|
|
18
|
|
19 <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/>
|
14
|
20 <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
|
12
|
21 </inputs>
|
|
22
|
|
23
|
|
24 <outputs>
|
|
25 <data format="tabular" name="output" />
|
|
26 </outputs>
|
|
27
|
14
|
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_pproph_protproph.prot.xml" format="protxml"/>
|
|
32 <output name="output" format="tabular">
|
|
33 <assert_contents>
|
|
34 <has_text text="AVQKYLTAHEQSK" />
|
|
35 </assert_contents>
|
|
36 </output>
|
|
37 </test>
|
|
38 </tests>
|
|
39
|
12
|
40
|
|
41 <help>
|
|
42
|
|
43 **What it does**
|
|
44
|
|
45 Converts a ProtXML file to a tab separated table
|
|
46
|
|
47 </help>
|
|
48
|
|
49 </tool>
|