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comparison msgf2pin.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
parents 3a49065a05d6
children
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0:3a49065a05d6 1:86770eea5b09
1 <tool id="msgfplus2pin" name="MS-GF+ output to Pin converter" version="3.0"> 1 <tool id="msgfplus2pin" name="MS-GF+ output to Pin converter" version="3.0.1">
2 <description>to create Percolator input files</description> 2 <description>to create Percolator input files</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.0">percolator</requirement> 4 <requirement type="package" version="3.0">percolator</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:"/> 7 <exit_code range="1:"/>
8 </stdio> 8 </stdio>
9 <command> 9 <command><![CDATA[
10 msgf2pin -o $pinout -e $enzyme 10 mkdir target && mkdir decoy &&
11 #if $matches 11
12 -m $matches 12 #if $mzids.inputtype == "multi"
13 #for $key in $mzids.target.keys()
14 ln -s '$mzids.target[$key]' 'target/$key' &&
15 echo 'target/$key' >> targetmeta &&
16 #end for
17 #for $key in $mzids.decoy.keys()
18 ln -s '$mzids.decoy[$key]' 'decoy/$key' &&
19 echo 'decoy/$key' >> decoymeta &&
20 #end for
21 msgf2pin -o $pinout -e $enzyme
22 #if $matches
23 -m $matches
24 #end if
25 $aafreq $ptm $pngase $isotope targetmeta decoymeta
26
27 #else
28 ln -s '$mzids.target' 'target/$target.display_name' &&
29 ln -s '$mzids.decoy' 'decoy/$decoy.display_name' &&
30 msgf2pin -o $pinout -e $enzyme
31 #if $matches
32 -m $matches
33 #end if
34 $aafreq $ptm $pngase $isotope
35 'target/$mzids.target.display_name' 'decoy/$mzids.decoy.display_name'
13 #end if 36 #end if
14 $aafreq $ptm $pngase $isotope 37 ]]></command>
15 "$target" "$decoy"
16 </command>
17 <inputs> 38 <inputs>
18 <param name="target" type="data" format="mzid,meta2pin" label="Target MSGF+ results or metafile pointing to them" /> 39 <conditional name="mzids">
19 <param name="decoy" type="data" format="mzid,meta2pin" label="Decoy MSGF+ results or metafile pointing to them" /> 40 <param name="inputtype" type="select" display="radio">
41 <option value="single">Single mzIdentML</option>
42 <option value="multi">Multiple mzIdentMLs</option>
43 </param>
44 <when value="single">
45 <param name="target" type="data" format="mzid" label="Target MSGF+ results" />
46 <param name="decoy" type="data" format="mzid" label="Decoy MSGF+ results" />
47 </when>
48 <when value="multi">
49 <param name="target" type="data_collection" collection_type="list" format="mzid" label="Target MSGF+ results" />
50 <param name="decoy" type="data_collection" collection_type="list" format="mzid" label="Decoy MSGF+ results" />
51 </when>
52 </conditional>
20 <param name="enzyme" type="select" label="Enzyme used"> 53 <param name="enzyme" type="select" label="Enzyme used">
21 <option value="trypsin">trypsin</option> 54 <option value="trypsin">trypsin</option>
22 <option value="no_enzyme">no enzyme</option> 55 <option value="no_enzyme">no enzyme</option>
23 <option value="elastase">elastase</option> 56 <option value="elastase">elastase</option>
24 <option value="pepsin">pepsin</option> 57 <option value="pepsin">pepsin</option>
40 <outputs> 73 <outputs>
41 <data format="percin" name="pinout"/> 74 <data format="percin" name="pinout"/>
42 </outputs> 75 </outputs>
43 <tests> 76 <tests>
44 <test> 77 <test>
45 <param name="target" value="target.mzid"/> 78 <param name="mzids|inputtype" value="single" />
46 <param name="decoy" value="decoy.mzid"/> 79 <param name="mzids|target" value="target.mzid" />
80 <param name="mzids|decoy" value="decoy.mzid" />
47 <param name="ptm" value="true"/> 81 <param name="ptm" value="true"/>
48 <param name="matches" value="1"/> 82 <param name="matches" value="1"/>
49 <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" /> 83 <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" />
84 </test>
85 <test>
86 <param name="mzids|inputtype" value="multi" />
87 <param name="mzids|target">
88 <collection type="list">
89 <element name="target1" value="target.mzid" />
90 <element name="target2" value="target.mzid" />
91 </collection>
92 </param>
93 <param name="mzids|decoy">
94 <collection type="list">
95 <element name="decoy1" value="decoy.mzid" />
96 <element name="decoy2" value="decoy.mzid" />
97 </collection>
98 </param>
99 <param name="ptm" value="true"/>
100 <param name="matches" value="1"/>
101 <output name="pinout" value="percolatorInresult_multifractions.txt" compare="sim_size" delta="20" />
50 </test> 102 </test>
51 </tests> 103 </tests>
52 <help> 104 <help>
53 The percolator converter msgf2pin converts mzIdentML to input for percolator. 105 The percolator converter msgf2pin converts mzIdentML to input for percolator.
54 Target and decoy inputs are MzIdentML-files of MS-GF+ from 106 Target and decoy inputs are MzIdentML-files of MS-GF+ from
55 separate target and decoy searches. Internal MS-GF+ target/decoy 107 separate target and decoy searches. Internal MS-GF+ target/decoy
56 analysis should be turned off, and the addFeatures options turned on. 108 analysis should be turned off, and the addFeatures options turned on.
57 Multiple MzIdentML-files can be merged by replacing target and decoy 109 Multiple MzIdentML-files can be merged by passing lists of these.
58 filepaths with meta files. Meta files are text files containing the 110 For successful results, the different runs should be generated under
59 the paths of mzid-files, one path per line. For successful results, 111 similar conditions.
60 the different runs should be generated under similar conditions.
61 </help> 112 </help>
62 <citations> 113 <citations>
63 <citation type="doi">10.1021/pr400937n</citation> 114 <citation type="doi">10.1021/pr400937n</citation>
64 </citations> 115 </citations>
65 </tool> 116 </tool>