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comparison idconvert.xml @ 0:f073fd791784 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
author galaxyp
date Fri, 08 Apr 2016 16:01:32 -0400
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children cd33680f08ef
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-1:000000000000 0:f073fd791784
1 <tool id="idconvert" name="idconvert" version="@VERSION@.0">
2 <description>Convert mass spectrometry identification files</description>
3
4 <macros>
5 <import>msconvert_macros.xml</import>
6 </macros>
7
8 <expand macro="generic_requirements" />
9
10 <command>
11 <![CDATA[
12 #set input_name
13 ln -s $input input.${input.extension}
14 idconvert input
15
16 ]]>
17 </command>
18
19 <inputs>
20 <conditional name="from">
21 <param name="from_format" type="select" label="Convert from">
22 <option value="mzid">mzIdentML (mzid)</option>
23 <option value="protxml">protXML (protxml)</option>
24 <option value="pepxml">pepXML (pepxml)</option>
25 </param>
26 <when value="mzid">
27 <param name="input" type="data" format="pepxml,protxml,mzid" label="MS mzIdentML (mzid)" />
28 </when>
29 <when value="protxml">
30 <param name="input" type="data" format="protxml" label="MS pepXML (pepxml)" />
31 <param name="pepxml" type="data" format="pepxml" label="MS Identification" />
32 </when>
33 <when value="pepxml">
34 <param name="input" type="data" format="pepxml" label="MS Identification" />
35 </when>
36 </conditional>
37 <param name="to_format" type="select" label="Convert to">
38 <option value="mzid">mzIdentML (mzid)</option>
39 <option value="pepxml">pepXML (pepxml)</option>
40 <option value="text">text</option>
41 </param>
42 </inputs>
43
44 <tests>
45 </tests>
46 <help>
47 </help>
48 <expand macro="citations" />
49 </tool>