Mercurial > repos > galaxyp > msconvert
comparison idconvert/idconvert.xml @ 4:158a71ee5733 draft
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author | galaxyp |
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date | Wed, 07 Dec 2016 17:43:19 -0500 |
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3:987d73278bf9 | 4:158a71ee5733 |
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1 <tool id="idconvert" name="idconvert" version="@VERSION@.0"> | |
2 <description>Convert mass spectrometry identification files</description> | |
3 <macros> | |
4 <import>msconvert_macros.xml</import> | |
5 </macros> | |
6 <expand macro="generic_requirements" /> | |
7 <stdio> | |
8 <exit_code range="1:" /> | |
9 <regex match="Error" | |
10 source="both" | |
11 level="fatal" | |
12 description="Error" /> | |
13 </stdio> | |
14 <command> | |
15 <![CDATA[ | |
16 #import os.path | |
17 #set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')]) | |
18 ln -s "$from.input" "$input_name" && | |
19 idconvert $input_name | |
20 #if str($to_format) == 'pep.xml': | |
21 --pepXML | |
22 #elif str($to_format) == 'text': | |
23 --text | |
24 #end if | |
25 --outdir outdir | |
26 && cp outdir/* $output | |
27 ]]> | |
28 </command> | |
29 <inputs> | |
30 <conditional name="from"> | |
31 <param name="from_format" type="select" label="Convert from"> | |
32 <option value="mzid">mzIdentML (mzid)</option> | |
33 <option value="pepxml">pepXML (pepxml)</option> | |
34 <option value="protxml">protXML (protxml)</option> | |
35 </param> | |
36 <when value="mzid"> | |
37 <param name="input" type="data" format="pepxml,protxml,mzid" label="MS mzIdentML (mzid)" /> | |
38 </when> | |
39 <when value="protxml"> | |
40 <param name="input" type="data" format="protxml" label="MS pepXML (pepxml)" /> | |
41 <param name="pepxml" type="data" format="pepxml" multiple="true" label="MS Identification" /> | |
42 </when> | |
43 <when value="pepxml"> | |
44 <param name="input" type="data" format="pepxml" label="MS Identification" /> | |
45 </when> | |
46 </conditional> | |
47 <param name="to_format" type="select" label="Convert to"> | |
48 <option value="mzid">mzIdentML (mzid)</option> | |
49 <option value="pep.xml">pepXML (pepxml)</option> | |
50 <option value="text">text</option> | |
51 </param> | |
52 </inputs> | |
53 <outputs> | |
54 <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}"> | |
55 <change_format> | |
56 <when input="to_format" value="pep.xml" format="pepxml" /> | |
57 <when input="to_format" value="text" format="txt" /> | |
58 </change_format> | |
59 </data> | |
60 </outputs> | |
61 <tests> | |
62 <test> | |
63 <param name="input" value="Rpal_01.pepXML" /> | |
64 <param name="from_format" value="pepxml" /> | |
65 <param name="to_format" value="mzid" /> | |
66 <output name="output_psms"> | |
67 <assert_contents> | |
68 <has_text text="MzIdentML" /> | |
69 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> | |
70 </assert_contents> | |
71 </output> | |
72 </test> | |
73 <test> | |
74 <param name="input" value="Rpal_01.mzid" /> | |
75 <param name="from_format" value="mzid" /> | |
76 <param name="to_format" value="pep.xml" /> | |
77 <output name="output_psms"> | |
78 <assert_contents> | |
79 <has_text text="msms_pipeline_analysis" /> | |
80 <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> | |
81 </assert_contents> | |
82 </output> | |
83 </test> | |
84 </tests> | |
85 <help> | |
86 <![CDATA[ | |
87 idconvert [options] [filemasks] | |
88 Convert mass spec identification file formats. | |
89 | |
90 Return value: # of failed files. | |
91 | |
92 Options: | |
93 -f [ --filelist ] arg : specify text file containing filenames | |
94 -o [ --outdir ] arg (=.) : set output directory ('-' for stdout) [.] | |
95 -c [ --config ] arg : configuration file (optionName=value) | |
96 -e [ --ext ] arg : set extension for output files [mzid|pepXML|txt] | |
97 --mzIdentML : write mzIdentML format [default] | |
98 --pepXML : write pepXML format | |
99 --text : write hierarchical text format | |
100 -v [ --verbose ] : display detailed progress information | |
101 Examples: | |
102 | |
103 # convert sequest.pepXML to sequest.mzid | |
104 idconvert sequest.pepXML | |
105 | |
106 # convert sequest.protXML to sequest.mzid | |
107 # Also reads any pepXML file referenced in the | |
108 # protXML file if available. If the protXML | |
109 # file has been moved from its original location, | |
110 # the pepXML will still be found if it has also | |
111 # been moved to the same position relative to the | |
112 # protXML file. This relative position is determined | |
113 # by reading the protXML protein_summary:summary_xml | |
114 # and protein_summary_header:source_files values. | |
115 idconvert sequest.protXML | |
116 | |
117 # convert mascot.mzid to mascot.pepXML | |
118 idconvert mascot.mzid --pepXML | |
119 | |
120 ]]> | |
121 </help> | |
122 <expand macro="citations" /> | |
123 </tool> |