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comparison pout2mzid.xml @ 1:86770eea5b09 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
author galaxyp
date Sat, 04 Mar 2017 20:36:03 -0500
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0:3a49065a05d6 1:86770eea5b09
1 <tool id="pout2mzid" name="Pout2mzid" version="0.3.03">
2 <description>add Percolator scoring to mzIdentML</description>
3 <requirements>
4 <requirement type="package" version="0.3.03">pout2mzid</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:"/>
8 </stdio>
9 <command><![CDATA[
10 #if $mzid.multifile == "true"
11 mkdir p2m_mzid_in &&
12 #set digits = "0" + str(len(str(len($mzid.mzids.keys()))))
13 #for $i, $fn in $enumerate($mzid.mzids.keys())
14 #set prefixnum = format($i, $digits)
15 ln -s '$mzid.mzids[$fn]' 'p2m_mzid_in/$fn' &&
16 #end for
17 ls p2m_mzid_in > infiles.txt &&
18 pout2mzid -p '$percout' -i p2m_mzid_in -f infiles.txt -o p2m_result -c _perco
19
20 #else
21 ln -s '$mzid.mzidsingle' '$mzid.mzidsingle.display_name' &&
22 pout2mzid -p '$percout' -m '$mzid.mzidsingle.display_name'
23 #end if
24
25 #if $targetdecoy == "decoy"
26 -d
27 #end if
28 #if $schemaskip
29 -v
30 #end if
31 #if $mzid.multifile == "false"
32 > '$output_single'
33 #end if
34 ]]></command>
35 <inputs>
36 <param name="percout" type="data" format="percout" label="Percolator output"/>
37 <conditional name="mzid">
38 <param name="multifile" type="select" display="radio" label="Multiple mzIdentML files?">
39 <option value="true">Yes</option>
40 <option value="false" selected="true">No</option>
41 </param>
42 <when value="true">
43 <param name="mzids" type="data_collection" collection_type="list" format="mzid" label="mzIdentML from MSGF+" />
44 </when>
45 <when value="false">
46 <param name="mzidsingle" type="data" format="mzid" label="mzIdentML from MSGF+" />
47 </when>
48 </conditional>
49 <param name="targetdecoy" type="select" display="radio" label="Which features to add to mzIdentML">
50 <option value="target" selected="true">Target</option>
51 <option value="decoy">Decoy</option>
52 </param>
53 <param name="schemaskip" type="boolean" label="Skip percolator schema validation?" />
54 </inputs>
55 <outputs>
56 <data name="output_single" format="mzid">
57 <filter>mzid['multifile'] == "false"</filter>
58 </data>
59 <collection name="output_multi" type="list">
60 <filter>mzid['multifile'] == "true"</filter>
61 <discover_datasets pattern="__designation__" ext="mzid" directory="p2m_result" />
62 </collection>
63
64 </outputs>
65 <tests>
66 <test>
67 <param name="percout" value="percolatorOut.xml" />
68 <param name="mzid|multifile" value="false" />
69 <param name="mzid|mzidsingle" value="dataset_2.mzid" />
70 <param name="targetdecoy" value="target" />
71 <param name="schemaskip" value="true" />
72 <output name="output_single" value="target_ds2_withperco.mzid" />
73 </test>
74 <test>
75 <param name="percout" value="percolatorOut.xml" />
76 <param name="mzid|multifile" value="true" />
77 <param name="mzid|mzids">
78 <collection type="list">
79 <element name="dataset_2.mzid" value="dataset_2.mzid" />
80 <element name="dataset_3.mzid" value="dataset_2.mzid" />
81 </collection>
82 </param>
83 <param name="targetdecoy" value="target" />
84 <param name="schemaskip" value="true" />
85 <output_collection name="output_multi" type="list">
86 <element name="dataset_2_perco.mzid" value="target_ds2_withperco.mzid" />
87 <element name="dataset_3_perco.mzid" value="target_ds3_withperco.mzid" />
88 </output_collection>
89 </test>
90 </tests>
91 <help>Pout2Mzid extracts statistics from a percolator input file, and writes them to the mzIdentML file(s) that have been used
92 to generate the percolator data. You may either pass multiple mzIdentML files in a list and one percolator file, or a single one.
93 </help>
94 </tool>