Mercurial > repos > galaxyp > msconvert

annotate idconvert/idconvert.xml @ 4:158a71ee5733 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author galaxyp
date Wed, 07 Dec 2016 17:43:19 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
1 <tool id="idconvert" name="idconvert" version="@VERSION@.0">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
2 <description>Convert mass spectrometry identification files</description>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
3 <macros>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
4 <import>msconvert_macros.xml</import>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
5 </macros>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
6 <expand macro="generic_requirements" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
7 <stdio>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
8 <exit_code range="1:" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
9 <regex match="Error"
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
10 source="both"
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
11 level="fatal"
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
12 description="Error" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
13 </stdio>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
14 <command>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
15 <![CDATA[
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
16 #import os.path
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
17 #set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')])
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
18 ln -s "$from.input" "$input_name" &&
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
19 idconvert $input_name
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
20 #if str($to_format) == 'pep.xml':
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
21 --pepXML
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
22 #elif str($to_format) == 'text':
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
23 --text
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
24 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
25 --outdir outdir
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
26 && cp outdir/* $output
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
27 ]]>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
28 </command>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
29 <inputs>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
30 <conditional name="from">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
31 <param name="from_format" type="select" label="Convert from">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
32 <option value="mzid">mzIdentML (mzid)</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
33 <option value="pepxml">pepXML (pepxml)</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
34 <option value="protxml">protXML (protxml)</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
35 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
36 <when value="mzid">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
37 <param name="input" type="data" format="pepxml,protxml,mzid" label="MS mzIdentML (mzid)" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
38 </when>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
39 <when value="protxml">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
40 <param name="input" type="data" format="protxml" label="MS pepXML (pepxml)" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
41 <param name="pepxml" type="data" format="pepxml" multiple="true" label="MS Identification" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
42 </when>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
43 <when value="pepxml">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
44 <param name="input" type="data" format="pepxml" label="MS Identification" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
45 </when>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
46 </conditional>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
47 <param name="to_format" type="select" label="Convert to">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
48 <option value="mzid">mzIdentML (mzid)</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
49 <option value="pep.xml">pepXML (pepxml)</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
50 <option value="text">text</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
51 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
52 </inputs>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
53 <outputs>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
54 <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
55 <change_format>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
56 <when input="to_format" value="pep.xml" format="pepxml" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
57 <when input="to_format" value="text" format="txt" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
58 </change_format>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
59 </data>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
60 </outputs>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
61 <tests>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
62 <test>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
63 <param name="input" value="Rpal_01.pepXML" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
64 <param name="from_format" value="pepxml" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
65 <param name="to_format" value="mzid" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
66 <output name="output_psms">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
67 <assert_contents>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
68 <has_text text="MzIdentML" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
69 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
70 </assert_contents>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
71 </output>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
72 </test>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
73 <test>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
74 <param name="input" value="Rpal_01.mzid" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
75 <param name="from_format" value="mzid" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
76 <param name="to_format" value="pep.xml" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
77 <output name="output_psms">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
78 <assert_contents>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
79 <has_text text="msms_pipeline_analysis" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
80 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
81 </assert_contents>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
82 </output>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
83 </test>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
84 </tests>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
85 <help>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
86 <![CDATA[
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
87 idconvert [options] [filemasks]
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
88 Convert mass spec identification file formats.
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
89
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
90 Return value: # of failed files.
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
91
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
92 Options:
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
93 -f [ --filelist ] arg : specify text file containing filenames
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
94 -o [ --outdir ] arg (=.) : set output directory ('-' for stdout) [.]
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
95 -c [ --config ] arg : configuration file (optionName=value)
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
96 -e [ --ext ] arg : set extension for output files [mzid|pepXML|txt]
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
97 --mzIdentML : write mzIdentML format [default]
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
98 --pepXML : write pepXML format
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
99 --text : write hierarchical text format
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
100 -v [ --verbose ] : display detailed progress information
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
101 Examples:
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
102
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
103 # convert sequest.pepXML to sequest.mzid
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
104 idconvert sequest.pepXML
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
105
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
106 # convert sequest.protXML to sequest.mzid
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
107 # Also reads any pepXML file referenced in the
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
108 # protXML file if available. If the protXML
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
109 # file has been moved from its original location,
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
110 # the pepXML will still be found if it has also
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
111 # been moved to the same position relative to the
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
112 # protXML file. This relative position is determined
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
113 # by reading the protXML protein_summary:summary_xml
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
114 # and protein_summary_header:source_files values.
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
115 idconvert sequest.protXML
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
116
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
117 # convert mascot.mzid to mascot.pepXML
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
118 idconvert mascot.mzid --pepXML
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
119
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
120 ]]>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
121 </help>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
122 <expand macro="citations" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
123 </tool>