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comparison idconvert.xml @ 1:cd33680f08ef draft default tip

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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 06:19:49 -0500
parents f073fd791784
children
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0:f073fd791784 1:cd33680f08ef
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 3 <requirements>
4 <macros> 4 <requirement type="package" version="3.0.9992">proteowizard</requirement>
5 <import>msconvert_macros.xml</import> 5 </requirements>
6 </macros> 6 <stdio>
7 7 <exit_code range="1:" />
8 <expand macro="generic_requirements" /> 8 <regex match="Error"
9 9 source="both"
10 level="fatal"
11 description="Error" />
12 </stdio>
10 <command> 13 <command>
11 <![CDATA[ 14 <![CDATA[
12 #set input_name 15 #import os.path
13 ln -s $input input.${input.extension} 16 #set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')])
14 idconvert input 17 ln -s '$from.input' '$input_name' &&
15 18 idconvert '$input_name'
19 #if str($to_format) == 'pep.xml':
20 --pepXML
21 #elif str($to_format) == 'text':
22 --text
23 #end if
24 --outdir 'outdir'
25 && cp outdir/* '$output'
16 ]]> 26 ]]>
17 </command> 27 </command>
18
19 <inputs> 28 <inputs>
20 <conditional name="from"> 29 <conditional name="from">
21 <param name="from_format" type="select" label="Convert from"> 30 <param name="from_format" type="select" label="Convert from">
22 <option value="mzid">mzIdentML (mzid)</option> 31 <option value="mzid">mzIdentML (mzid)</option>
32 <option value="pepxml">pepXML (pepxml)</option>
23 <option value="protxml">protXML (protxml)</option> 33 <option value="protxml">protXML (protxml)</option>
24 <option value="pepxml">pepXML (pepxml)</option>
25 </param> 34 </param>
26 <when value="mzid"> 35 <when value="mzid">
27 <param name="input" type="data" format="pepxml,protxml,mzid" label="MS mzIdentML (mzid)" /> 36 <param name="input" type="data" format="pepxml,protxml,mzid" label="MS mzIdentML (mzid)" />
28 </when> 37 </when>
29 <when value="protxml"> 38 <when value="protxml">
30 <param name="input" type="data" format="protxml" label="MS pepXML (pepxml)" /> 39 <param name="input" type="data" format="protxml" label="MS pepXML (pepxml)" />
31 <param name="pepxml" type="data" format="pepxml" label="MS Identification" /> 40 <param name="pepxml" type="data" format="pepxml" multiple="true" label="MS Identification" />
32 </when> 41 </when>
33 <when value="pepxml"> 42 <when value="pepxml">
34 <param name="input" type="data" format="pepxml" label="MS Identification" /> 43 <param name="input" type="data" format="pepxml" label="MS Identification" />
35 </when> 44 </when>
36 </conditional> 45 </conditional>
37 <param name="to_format" type="select" label="Convert to"> 46 <param name="to_format" type="select" label="Convert to">
38 <option value="mzid">mzIdentML (mzid)</option> 47 <option value="mzid">mzIdentML (mzid)</option>
39 <option value="pepxml">pepXML (pepxml)</option> 48 <option value="pep.xml">pepXML (pepxml)</option>
40 <option value="text">text</option> 49 <option value="text">text</option>
41 </param> 50 </param>
42 </inputs> 51 </inputs>
52 <outputs>
53 <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}">
54 <change_format>
55 <when input="to_format" value="pep.xml" format="pepxml" />
56 <when input="to_format" value="text" format="txt" />
57 </change_format>
58 </data>
59 </outputs>
60 <tests>
61 <test>
62 <param name="input" value="Rpal_01.pepXML" />
63 <param name="from_format" value="pepxml" />
64 <param name="to_format" value="mzid" />
65 <output name="output">
66 <assert_contents>
67 <has_text text="MzIdentML" />
68 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
69 </assert_contents>
70 </output>
71 </test>
72 <test>
73 <param name="input" value="Rpal_01.mzid" />
74 <param name="from_format" value="mzid" />
75 <param name="to_format" value="pep.xml" />
76 <output name="output">
77 <assert_contents>
78 <has_text text="msms_pipeline_analysis" />
79 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
80 </assert_contents>
81 </output>
82 </test>
83 </tests>
84 <help>
85 <![CDATA[
86 idconvert [options] [filemasks]
87 Convert mass spec identification file formats.
43 88
44 <tests> 89 Return value: # of failed files.
45 </tests> 90
46 <help> 91 Options:
47 </help> 92 -f [ --filelist ] arg : specify text file containing filenames
48 <expand macro="citations" /> 93 -o [ --outdir ] arg (=.) : set output directory ('-' for stdout) [.]
94 -c [ --config ] arg : configuration file (optionName=value)
95 -e [ --ext ] arg : set extension for output files [mzid|pepXML|txt]
96 --mzIdentML : write mzIdentML format [default]
97 --pepXML : write pepXML format
98 --text : write hierarchical text format
99 -v [ --verbose ] : display detailed progress information
100 Examples:
101
102 # convert sequest.pepXML to sequest.mzid
103 idconvert sequest.pepXML
104
105 # convert sequest.protXML to sequest.mzid
106 # Also reads any pepXML file referenced in the
107 # protXML file if available. If the protXML
108 # file has been moved from its original location,
109 # the pepXML will still be found if it has also
110 # been moved to the same position relative to the
111 # protXML file. This relative position is determined
112 # by reading the protXML protein_summary:summary_xml
113 # and protein_summary_header:source_files values.
114 idconvert sequest.protXML
115
116 # convert mascot.mzid to mascot.pepXML
117 idconvert mascot.mzid --pepXML
118
119 ]]>
120 </help>
121 <citations>
122 <citation type="doi">10.1093/bioinformatics/btn323</citation>
123 </citations>
49 </tool> 124 </tool>