Mercurial > repos > lecorguille > camera_annotate

comparison macros.xml @ 13:1c30ff90f3ae draft

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planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
author lecorguille
date Fri, 07 Apr 2017 07:42:18 -0400
parents 9c037181588e
children 225cb8347572
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12:9c037181588e 13:1c30ff90f3ae
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
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="1.26.0">bioconductor-camera</requirement> 6 <requirement type="package" version="1.26.0">bioconductor-camera</requirement>
7 <requirement type="package" version="2.26.0">bioconductor-multtest</requirement> 7 <requirement type="package" version="2.26.0">bioconductor-multtest</requirement>
8 <requirement type="package" version="1.1_4">r-batch</requirement> 8 <requirement type="package" version="1.1_4">r-batch</requirement>
9 <requirement type="package" version="1.6.27">libpng</requirement> 9 <requirement type="package" version="1.3.23">graphicsmagick</requirement>
10 <requirement type="package" version="1.3.20">graphicsmagick</requirement>
11 </requirements> 10 </requirements>
12 </xml> 11 </xml>
13 <xml name="stdio"> 12 <xml name="stdio">
14 <stdio> 13 <stdio>
15 <exit_code range="1" level="fatal" /> 14 <exit_code range="1" level="fatal" />
17 </xml> 16 </xml>
18 17
19 <token name="@COMMAND_CAMERA_SCRIPT@"> 18 <token name="@COMMAND_CAMERA_SCRIPT@">
20 LANG=C Rscript $__tool_directory__/CAMERA.r 19 LANG=C Rscript $__tool_directory__/CAMERA.r
21 </token> 20 </token>
22 21
23 <!-- zipfile load for planemo test --> 22 <!-- raw file load for planemo test -->
24 <token name="@COMMAND_ZIPFILE_LOAD@"> 23 <token name="@COMMAND_FILE_LOAD@">
25 #if $zipfile_load_conditional.zipfile_load_select == "yes": 24 #if $file_load_section.file_load_conditional.file_load_select == "yes":
26 #if $zipfile_load_conditional.zip_file: 25 #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"):
27 zipfile $zipfile_load_conditional.zip_file 26 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
27 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
28 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
29 #else
30 zipfile '$file_load_section.file_load_conditional.input'
28 #end if 31 #end if
29 #end if 32 #end if
30 </token> 33 </token>
31 <xml name="zipfile_load"> 34
32 <conditional name="zipfile_load_conditional"> 35 <xml name="input_file_load">
33 <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." > 36 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
34 <option value="no" >no need</option> 37 <conditional name="file_load_conditional">
35 <option value="yes" selected="peakgroups">yes</option> 38 <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." >
39 <option value="no" >no need</option>
40 <option value="yes" >yes</option>
41 </param>
42 <when value="no">
43 </when>
44 <when value="yes">
45 <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." />
46 </when>
47 </conditional>
48 </section>
49 </xml>
50
51 <xml name="test_file_load_zip">
52 <section name="file_load_section">
53 <conditional name="file_load_conditional">
54 <param name="file_load_select" value="yes" />
55 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
56 </conditional>
57 </section>
58 </xml>
59
60 <xml name="test_file_load_single">
61 <section name="file_load_section">
62 <conditional name="file_load_conditional">
63 <param name="file_load_select" value="yes" />
64 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
65 </conditional>
66 </section>
67 </xml>
68
69 <!-- peaklist export option management -->
70 <token name="@COMMAND_PEAKLIST@">
71 convertRTMinute $export.convertRTMinute
72 numDigitsMZ $export.numDigitsMZ
73 numDigitsRT $export.numDigitsRT
74 intval $export.intval
75 </token>
76
77 <xml name="input_peaklist">
78 <section name="export" title="Export options">
79 <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"/>
80 <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" />
81 <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" />
82 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
83 <option value="into" selected="true">into</option>
84 <option value="maxo" >maxo</option>
85 <option value="intb">intb</option>
36 </param> 86 </param>
37 <when value="no"> 87 </section>
38 </when> 88 </xml>
39 <when value="yes"> 89
40 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> 90 <xml name="test_peaklist">
41 </when> 91 <section name="export">
92 <param name="convertRTMinute" value="True"/>
93 <param name="numDigitsMZ" value="4" />
94 <param name="numDigitsRT" value="1" />
95 <param name="intval" value="into"/>
96 </section>
97 </xml>
98
99 <!-- annotate_diffreport <test> commun part -->
100 <xml name="test_annotate_diffreport">
101 <section name="groupfwhm">
102 <param name="sigma" value="6"/>
103 <param name="perfwhm" value="0.6"/>
104 </section>
105 <section name="findisotopes">
106 <param name="maxcharge" value="3"/>
107 <param name="maxiso" value="4"/>
108 <param name="minfrac" value="0.5"/>
109 </section>
110 <section name="findgeneral">
111 <param name="ppm" value="5"/>
112 <param name="mzabs" value="0.015"/>
113 <param name="max_peaks" value="100"/>
114 </section>
115 <section name="diffreport">
116 <conditional name="options">
117 <param name="option" value="show"/>
118 <param name="eicmax" value="200"/>
119 <param name="eicwidth" value="200"/>
120 <param name="value" value="into"/>
121 <param name="h" value="480"/>
122 <param name="w" value="640"/>
123 <param name="mzdec" value="2"/>
124 <param name="sortpval" value="False"/>
125 </conditional>
126 </section>
127 <expand macro="test_peaklist"/>
128 </xml>
129
130 <xml name="test_annotate_quick_false">
131 <param name="quick" value="FALSE"/>
132 <section name="groupcorr">
133 <param name="cor_eic_th" value="0.75"/>
134 <param name="graphMethod" value="hcs"/>
135 <param name="pval" value="0.05"/>
136 <param name="calcCiS" value="True"/>
137 <param name="calcIso" value="False"/>
138 <param name="calcCaS" value="False"/>
139 </section>
140 </xml>
141
142 <xml name="test_annotate_quick_true">
143 <conditional name="quick_block">
144 <param name="quick" value="TRUE"/>
42 </conditional> 145 </conditional>
43 </xml> 146 </xml>
44 147
45 <token name="@HELP_AUTHORS@"> 148 <token name="@HELP_AUTHORS@">
46 .. class:: infomark 149 .. class:: infomark
47 150
48 **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 151 **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
49 152
50 .. class:: infomark 153 .. class:: infomark
51 154
52 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] 155 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
53 156