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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
author galaxyp
date Sat, 23 Feb 2019 06:21:11 -0500
parents 9e6e840d6b52
children
comparison
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1:9e6e840d6b52 2:edb33e8224c6
1 <tool id="idconvert" name="idconvert" version="@VERSION@.0"> 1 <tool id="idconvert" name="idconvert" version="@VERSION@.0">
2 <description>Convert mass spectrometry identification files</description> 2 <description>Convert mass spectrometry identification files</description>
3 <macros> 3 <requirements>
4 <import>msconvert_macros.xml</import> 4 <requirement type="package" version="3.0.9992">proteowizard</requirement>
5 </macros> 5 </requirements>
6 <expand macro="generic_requirements" />
7 <stdio> 6 <stdio>
8 <exit_code range="1:" /> 7 <exit_code range="1:" />
9 <regex match="Error" 8 <regex match="Error"
10 source="both" 9 source="both"
11 level="fatal" 10 level="fatal"
13 </stdio> 12 </stdio>
14 <command> 13 <command>
15 <![CDATA[ 14 <![CDATA[
16 #import os.path 15 #import os.path
17 #set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')]) 16 #set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')])
18 ln -s "$from.input" "$input_name" && 17 ln -s '$from.input' '$input_name' &&
19 idconvert $input_name 18 idconvert '$input_name'
20 #if str($to_format) == 'pep.xml': 19 #if str($to_format) == 'pep.xml':
21 --pepXML 20 --pepXML
22 #elif str($to_format) == 'text': 21 #elif str($to_format) == 'text':
23 --text 22 --text
24 #end if 23 #end if
25 --outdir outdir 24 --outdir 'outdir'
26 && cp outdir/* $output 25 && cp outdir/* '$output'
27 ]]> 26 ]]>
28 </command> 27 </command>
29 <inputs> 28 <inputs>
30 <conditional name="from"> 29 <conditional name="from">
31 <param name="from_format" type="select" label="Convert from"> 30 <param name="from_format" type="select" label="Convert from">
47 <param name="to_format" type="select" label="Convert to"> 46 <param name="to_format" type="select" label="Convert to">
48 <option value="mzid">mzIdentML (mzid)</option> 47 <option value="mzid">mzIdentML (mzid)</option>
49 <option value="pep.xml">pepXML (pepxml)</option> 48 <option value="pep.xml">pepXML (pepxml)</option>
50 <option value="text">text</option> 49 <option value="text">text</option>
51 </param> 50 </param>
52 </inputs> 51 </inputs>
53 <outputs> 52 <outputs>
54 <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}"> 53 <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}">
55 <change_format> 54 <change_format>
56 <when input="to_format" value="pep.xml" format="pepxml" /> 55 <when input="to_format" value="pep.xml" format="pepxml" />
57 <when input="to_format" value="text" format="txt" /> 56 <when input="to_format" value="text" format="txt" />
58 </change_format> 57 </change_format>
59 </data> 58 </data>
60 </outputs> 59 </outputs>
61 <tests> 60 <tests>
62 <test> 61 <test>
63 <param name="input" value="Rpal_01.pepXML" /> 62 <param name="input" value="Rpal_01.pepXML" />
64 <param name="from_format" value="pepxml" /> 63 <param name="from_format" value="pepxml" />
65 <param name="to_format" value="mzid" /> 64 <param name="to_format" value="mzid" />
66 <output name="output_psms"> 65 <output name="output">
67 <assert_contents> 66 <assert_contents>
68 <has_text text="MzIdentML" /> 67 <has_text text="MzIdentML" />
69 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> 68 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
70 </assert_contents> 69 </assert_contents>
71 </output> 70 </output>
72 </test> 71 </test>
73 <test> 72 <test>
74 <param name="input" value="Rpal_01.mzid" /> 73 <param name="input" value="Rpal_01.mzid" />
75 <param name="from_format" value="mzid" /> 74 <param name="from_format" value="mzid" />
76 <param name="to_format" value="pep.xml" /> 75 <param name="to_format" value="pep.xml" />
77 <output name="output_psms"> 76 <output name="output">
78 <assert_contents> 77 <assert_contents>
79 <has_text text="msms_pipeline_analysis" /> 78 <has_text text="msms_pipeline_analysis" />
80 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> 79 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
81 </assert_contents> 80 </assert_contents>
82 </output> 81 </output>
83 </test> 82 </test>
84 </tests> 83 </tests>
85 <help> 84 <help>
86 <![CDATA[ 85 <![CDATA[
87 idconvert [options] [filemasks] 86 idconvert [options] [filemasks]
88 Convert mass spec identification file formats. 87 Convert mass spec identification file formats.
89 88
90 Return value: # of failed files. 89 Return value: # of failed files.
116 115
117 # convert mascot.mzid to mascot.pepXML 116 # convert mascot.mzid to mascot.pepXML
118 idconvert mascot.mzid --pepXML 117 idconvert mascot.mzid --pepXML
119 118
120 ]]> 119 ]]>
121 </help> 120 </help>
122 <expand macro="citations" /> 121 <citations>
122 <citation type="doi">10.1093/bioinformatics/btn323</citation>
123 </citations>
123 </tool> 124 </tool>