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comparison macros.xml @ 0:139ff66b0b5d draft

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planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464
author workflow4metabolomics
date Fri, 26 Jul 2019 16:49:18 -0400
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children ea15115a5b3f
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-1:000000000000 0:139ff66b0b5d
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="0.4_3">r-snow</requirement>
6 <requirement type="package" version="1.38.1">bioconductor-camera</requirement>
7 <requirement type="package" version="2.38.0">bioconductor-multtest</requirement>
8 <requirement type="package" version="1.1_4">r-batch</requirement>
9 <requirement type="package" version="1.3.31">graphicsmagick</requirement>
10 </requirements>
11 </xml>
12 <xml name="stdio">
13 <stdio>
14 <exit_code range="1" level="fatal" />
15 </stdio>
16 </xml>
17
18 <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
19
20 <!-- raw file load for planemo test -->
21 <token name="@COMMAND_FILE_LOAD@">
22 #if $file_load_section.file_load_conditional.file_load_select == "yes":
23 #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"):
24 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
25 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
26 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
27 #else
28 zipfile '$file_load_section.file_load_conditional.input'
29 #end if
30 #end if
31 </token>
32
33 <xml name="input_file_load">
34 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
35 <conditional name="file_load_conditional">
36 <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." >
37 <option value="no" >no need</option>
38 <option value="yes" >yes</option>
39 </param>
40 <when value="no">
41 </when>
42 <when value="yes">
43 <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." />
44 </when>
45 </conditional>
46 </section>
47 </xml>
48
49 <xml name="test_file_load_zip">
50 <section name="file_load_section">
51 <conditional name="file_load_conditional">
52 <param name="file_load_select" value="yes" />
53 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
54 </conditional>
55 </section>
56 </xml>
57
58 <xml name="test_file_load_single">
59 <section name="file_load_section">
60 <conditional name="file_load_conditional">
61 <param name="file_load_select" value="yes" />
62 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
63 </conditional>
64 </section>
65 </xml>
66
67 <!-- peaklist export option management -->
68 <token name="@COMMAND_PEAKLIST@">
69 convertRTMinute $export.convertRTMinute
70 numDigitsMZ $export.numDigitsMZ
71 numDigitsRT $export.numDigitsRT
72 intval $export.intval
73 </token>
74
75 <xml name="input_peaklist">
76 <section name="export" title="Export options">
77 <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"/>
78 <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" />
79 <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" />
80 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
81 <option value="into" selected="true">into</option>
82 <option value="maxo" >maxo</option>
83 <option value="intb">intb</option>
84 </param>
85 </section>
86 </xml>
87
88 <xml name="test_peaklist">
89 <section name="export">
90 <param name="convertRTMinute" value="True"/>
91 <param name="numDigitsMZ" value="4" />
92 <param name="numDigitsRT" value="1" />
93 <param name="intval" value="into"/>
94 </section>
95 </xml>
96
97 <!-- annotate_diffreport <test> commun part -->
98 <xml name="test_annotate_diffreport">
99 <section name="groupfwhm">
100 <param name="sigma" value="6"/>
101 <param name="perfwhm" value="0.6"/>
102 </section>
103 <section name="findisotopes">
104 <param name="maxcharge" value="3"/>
105 <param name="maxiso" value="4"/>
106 <param name="minfrac" value="0.5"/>
107 </section>
108 <section name="findgeneral">
109 <param name="ppm" value="5"/>
110 <param name="mzabs" value="0.015"/>
111 <param name="max_peaks" value="100"/>
112 </section>
113 <section name="diffreport">
114 <conditional name="options">
115 <param name="option" value="show"/>
116 <param name="eicmax" value="200"/>
117 <param name="eicwidth" value="200"/>
118 <param name="value" value="into"/>
119 <param name="h" value="480"/>
120 <param name="w" value="640"/>
121 <param name="mzdec" value="2"/>
122 <param name="sortpval" value="False"/>
123 </conditional>
124 </section>
125 <expand macro="test_peaklist"/>
126 </xml>
127
128 <xml name="test_annotate_quick_false">
129 <param name="quick" value="FALSE"/>
130 <section name="groupcorr">
131 <param name="cor_eic_th" value="0.75"/>
132 <param name="graphMethod" value="hcs"/>
133 <param name="pval" value="0.05"/>
134 <param name="calcCiS" value="True"/>
135 <param name="calcIso" value="False"/>
136 <param name="calcCaS" value="False"/>
137 </section>
138 </xml>
139
140 <xml name="test_annotate_quick_true">
141 <conditional name="quick_block">
142 <param name="quick" value="TRUE"/>
143 </conditional>
144 </xml>
145
146 <token name="@HELP_AUTHORS@">
147 .. class:: infomark
148
149 **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
150
151 .. class:: infomark
152
153 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
154
155 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
156
157 ---------------------------------------------------
158
159 </token>
160
161
162 <xml name="citation">
163 <citations>
164 <citation type="doi">10.1021/ac202450g</citation>
165 <citation type="doi">10.1093/bioinformatics/btu813</citation>
166 </citations>
167 </xml>
168 </macros>