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comparison percolator_converters.xml @ 2:7a0951d0e13e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
author galaxyp
date Fri, 10 Mar 2017 03:20:52 -0500
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1:86770eea5b09 2:7a0951d0e13e
1 <tool id="percolator_input_converters" name="Search engine output to Pin converter" version="3.1">
2 <description>to create Percolator input files</description>
3 <requirements>
4 <requirement type="package" version="3.1">percolator</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:"/>
8 </stdio>
9 <command><![CDATA[
10 mkdir target && mkdir decoy &&
11
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 $searchengine -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 $searchengine -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'
36 #end if
37 ]]></command>
38 <inputs>
39 <param name="searchengine" type="select" label="Search engine used">
40 <option value="msgf2pin">MSGF+ (mzIdentML)</option>
41 <option value="tandem2pin">X!Tandem (tandem)</option>
42 <option value="sqt2pin">Crux (SQT output)</option>
43 </param>
44 <conditional name="mzids">
45 <param name="inputtype" type="select" display="radio">
46 <option value="single">Single mzIdentML</option>
47 <option value="multi">Multiple mzIdentMLs</option>
48 </param>
49 <when value="single">
50 <param name="target" type="data" format="mzid" label="Target MSGF+ results" />
51 <param name="decoy" type="data" format="mzid" label="Decoy MSGF+ results" />
52 </when>
53 <when value="multi">
54 <param name="target" type="data_collection" collection_type="list" format="mzid" label="Target MSGF+ results" />
55 <param name="decoy" type="data_collection" collection_type="list" format="mzid" label="Decoy MSGF+ results" />
56 </when>
57 </conditional>
58 <param name="enzyme" type="select" label="Enzyme used">
59 <option value="trypsin">trypsin</option>
60 <option value="no_enzyme">no enzyme</option>
61 <option value="elastase">elastase</option>
62 <option value="pepsin">pepsin</option>
63 <option value="proteinasek">proteinase K</option>
64 <option value="thermolysin">thermolysin</option>
65 <option value="chymotrypsin">chymotrypsin</option>
66 <option value="lys-n">lys-N</option>
67 <option value="lys-c">lys-C</option>
68 <option value="arg-c">arg-C</option>
69 <option value="asp-n">asp-N</option>
70 <option value="glu-c">glu-C</option>
71 </param>
72 <param name="matches" type="integer" optional="true" label="Max number of PSMs for a spectrum" />
73 <param name="aafreq" type="boolean" label="Calculate amino acid frequency features" truevalue="-a" falsevalue="" />
74 <param name="ptm" type="boolean" label="Calculate feature for number of PTMs" truevalue="-b" falsevalue="" />
75 <param name="pngase" type="boolean" label="Calculate feature based on N-linked glycosylation resulting from PNGaseF" truevalue="-N" falsevalue="" />
76 <param name="isotope" type="boolean" label="Calculate mass difference to closest isotope instead of avg. mass" truevalue="-M" falsevalue="" />
77 </inputs>
78 <outputs>
79 <data format="percin" name="pinout"/>
80 </outputs>
81 <tests>
82 <test>
83 <param name="mzids|inputtype" value="single" />
84 <param name="mzids|target" value="target.mzid" />
85 <param name="mzids|decoy" value="decoy.mzid" />
86 <param name="ptm" value="true"/>
87 <param name="matches" value="1"/>
88 <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" />
89 </test>
90 <test>
91 <param name="mzids|inputtype" value="multi" />
92 <param name="mzids|target">
93 <collection type="list">
94 <element name="target1" value="target.mzid" />
95 <element name="target2" value="target.mzid" />
96 </collection>
97 </param>
98 <param name="mzids|decoy">
99 <collection type="list">
100 <element name="decoy1" value="decoy.mzid" />
101 <element name="decoy2" value="decoy.mzid" />
102 </collection>
103 </param>
104 <param name="ptm" value="true"/>
105 <param name="matches" value="1"/>
106 <output name="pinout" value="percolatorInresult_multifractions.txt" compare="sim_size" delta="20" />
107 </test>
108 </tests>
109 <help>
110 The percolator converter msgf2pin converts mzIdentML to input for percolator.
111 Target and decoy inputs are MzIdentML-files of MS-GF+ from
112 separate target and decoy searches. Internal MS-GF+ target/decoy
113 analysis should be turned off, and the addFeatures options turned on.
114 Multiple MzIdentML-files can be merged by passing lists of these.
115 For successful results, the different runs should be generated under
116 similar conditions.
117 </help>
118 <citations>
119 <citation type="doi">10.1021/pr400937n</citation>
120 </citations>
121 </tool>