Mercurial > repos > lecorguille > xcms_fillpeaks

comparison macros.xml @ 11:de0d85537ee3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author lecorguille
date Fri, 07 Apr 2017 07:37:05 -0400
parents ee29f0a6e361
children dcb9041cb9ea
comparison
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10:6caa60dcc217 11:de0d85537ee3
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.4_1">r-snow</requirement> 5 <requirement type="package" version="0.4_1">r-snow</requirement>
6 <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> 6 <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
7 <requirement type="package" version="1.1_4">r-batch</requirement> 7 <requirement type="package" version="1.1_4">r-batch</requirement>
8 </requirements>
9 </xml>
10 <xml name="requirements_light">
11 <requirements>
12 <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
8 </requirements> 13 </requirements>
9 </xml> 14 </xml>
10 <xml name="stdio"> 15 <xml name="stdio">
11 <stdio> 16 <stdio>
12 <exit_code range="1" level="fatal" /> 17 <exit_code range="1" level="fatal" />
18 </token> 23 </token>
19 24
20 <token name="@COMMAND_LOG_EXIT@"> 25 <token name="@COMMAND_LOG_EXIT@">
21 ; 26 ;
22 return=\$?; 27 return=\$?;
23 mv log.txt $log; 28 mv log.txt '$log';
24 cat $log; 29 cat '$log';
25 sh -c "exit \$return" 30 sh -c "exit \$return"
26 </token> 31 </token>
27 32
28 <!-- zipfile load for planemo test --> 33 <!-- zipfile load for planemo test -->
29 34
30 <token name="@COMMAND_ZIPFILE_LOAD@"> 35 <token name="@COMMAND_FILE_LOAD@">
31 #if $zipfile_load_conditional.zipfile_load_select == "yes": 36 #if $file_load_section.file_load_conditional.file_load_select == "yes":
32 #if $zipfile_load_conditional.zip_file: 37 #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
33 zipfile $zipfile_load_conditional.zip_file 38 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
39 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
40
41 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
42 #else
43 zipfile '$file_load_section.file_load_conditional.input'
34 #end if 44 #end if
35 #end if 45 #end if
36 </token> 46 </token>
37 47
38 <xml name="zipfile_load"> 48 <xml name="input_file_load">
39 <conditional name="zipfile_load_conditional"> 49 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
40 <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." > 50 <conditional name="file_load_conditional">
41 <option value="no" >no need</option> 51 <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
42 <option value="yes">yes</option> 52 <option value="no" >no need</option>
43 </param> 53 <option value="yes" >yes</option>
44 <when value="no"> 54 </param>
55 <when value="no">
56 </when>
57 <when value="yes">
58 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
59 </when>
60 </conditional>
61 </section>
62 </xml>
63
64 <xml name="test_file_load_zip">
65 <section name="file_load_section">
66 <conditional name="file_load_conditional">
67 <param name="file_load_select" value="yes" />
68 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
69 </conditional>
70 </section>
71 </xml>
72
73 <xml name="test_file_load_single">
74 <section name="file_load_section">
75 <conditional name="file_load_conditional">
76 <param name="file_load_select" value="yes" />
77 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
78 </conditional>
79 </section>
80 </xml>
81
82 <token name="@COMMAND_PEAKLIST@">
83 #if $peaklist.peaklistBool
84 variableMetadataOutput '$variableMetadata'
85 dataMatrixOutput '$dataMatrix'
86 convertRTMinute $peaklist.convertRTMinute
87 numDigitsMZ $peaklist.numDigitsMZ
88 numDigitsRT $peaklist.numDigitsRT
89 intval $peaklist.intval
90 #end if
91 </token>
92
93 <xml name="input_peaklist">
94 <conditional name="peaklist">
95 <param name="peaklistBool" type="boolean" label="Get a Peak List" />
96 <when value="true">
97 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
98 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
99 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
100 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
101 <option value="into" selected="true">into</option>
102 <option value="maxo">maxo</option>
103 <option value="intb">intb</option>
104 </param>
45 </when> 105 </when>
46 <when value="yes"> 106 <when value="false" />
47 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
48 </when>
49 </conditional> 107 </conditional>
50 </xml> 108 </xml>
51 109
52 110 <xml name="output_peaklist" token_function="">
111 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv">
112 <filter>(peaklist['peaklistBool'])</filter>
113 </data>
114 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" >
115 <filter>(peaklist['peaklistBool'])</filter>
116 </data>
117 </xml>
53 118
54 <token name="@HELP_AUTHORS@"> 119 <token name="@HELP_AUTHORS@">
55 .. class:: infomark 120 .. class:: infomark
56 121
57 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu 122 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
58 123
59 .. class:: infomark 124 .. class:: infomark
60 125
61 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] 126 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
62 127