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comparison macros.xml @ 0:6aea0427511e draft default tip

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planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d
author workflow4metabolomics
date Sun, 24 Nov 2024 21:28:57 +0000
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comparison
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-1:000000000000 0:6aea0427511e
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">1.48.0</token>
4 <token name="@VERSION_SUFFIX@">1</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="0.4_3">r-snow</requirement>
8 <requirement type="package" version="1.2.6">bioconductor-genomeinfodbdata</requirement>
9 <requirement type="package" version="@TOOL_VERSION@">bioconductor-camera</requirement>
10 <requirement type="package" version="2.48.0">bioconductor-multtest</requirement>
11 <requirement type="package" version="1.1_5">r-batch</requirement>
12 <requirement type="package" version="1.3.26">graphicsmagick</requirement>
13 <requirement type="package" version="3.0">zip</requirement>
14 </requirements>
15 </xml>
16 <xml name="stdio">
17 <stdio>
18 <exit_code range="1" level="fatal" />
19 </stdio>
20 </xml>
21
22 <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
23
24 <!-- raw file load for planemo test -->
25 <token name="@COMMAND_FILE_LOAD@">
26 #if $file_load_section.file_load_conditional.file_load_select == "yes":
27 #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"):
28 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
29 #set singlefile_sampleName = ','.join( [ str( $single_file.element_identifier ) for $single_file in $file_load_section.file_load_conditional.input ] )
30 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
31 #else
32 zipfile '$file_load_section.file_load_conditional.input'
33 #end if
34 #end if
35 </token>
36
37 <xml name="input_file_load">
38 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
39 <conditional name="file_load_conditional">
40 <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.">
41 <option value="no">no need</option>
42 <option value="yes">yes</option>
43 </param>
44 <when value="no">
45 </when>
46 <when value="yes">
47 <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." />
48 </when>
49 </conditional>
50 </section>
51 </xml>
52
53 <xml name="test_file_load_zip">
54 <section name="file_load_section">
55 <conditional name="file_load_conditional">
56 <param name="file_load_select" value="yes" />
57 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
58 </conditional>
59 </section>
60 </xml>
61
62 <xml name="test_file_load_single">
63 <section name="file_load_section">
64 <conditional name="file_load_conditional">
65 <param name="file_load_select" value="yes" />
66 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
67 </conditional>
68 </section>
69 </xml>
70
71 <xml name="test_file_load_faahKO_15">
72 <section name="file_load_section">
73 <conditional name="file_load_conditional">
74 <param name="file_load_select" value="yes" />
75 <param name="input" value="wt15.CDF,ko15.CDF" ftype="netcdf" />
76 </conditional>
77 </section>
78 </xml>
79
80 <!-- peaklist export option management -->
81 <token name="@COMMAND_PEAKLIST@">
82 convertRTMinute $export.convertRTMinute
83 numDigitsMZ $export.numDigitsMZ
84 numDigitsRT $export.numDigitsRT
85 intval $export.intval
86 </token>
87
88 <xml name="input_peaklist">
89 <section name="export" title="Export options">
90 <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"/>
91 <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" />
92 <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" />
93 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
94 <option value="into" selected="true">into</option>
95 <option value="maxo">maxo</option>
96 <option value="intb">intb</option>
97 </param>
98 </section>
99 </xml>
100
101 <xml name="test_peaklist">
102 <section name="export">
103 <param name="convertRTMinute" value="True"/>
104 <param name="numDigitsMZ" value="4" />
105 <param name="numDigitsRT" value="1" />
106 <param name="intval" value="into"/>
107 </section>
108 </xml>
109
110 <!-- annotate_diffreport <test> commun part -->
111 <xml name="test_annotate_diffreport">
112 <section name="groupfwhm">
113 <param name="sigma" value="6"/>
114 <param name="perfwhm" value="0.6"/>
115 </section>
116 <section name="findisotopes">
117 <param name="maxcharge" value="3"/>
118 <param name="maxiso" value="4"/>
119 <param name="minfrac" value="0.5"/>
120 </section>
121 <section name="findgeneral">
122 <param name="ppm" value="5"/>
123 <param name="mzabs" value="0.015"/>
124 <param name="max_peaks" value="100"/>
125 </section>
126 <section name="diffreport">
127 <conditional name="options">
128 <param name="option" value="show"/>
129 <param name="eicmax" value="200"/>
130 <param name="eicwidth" value="200"/>
131 <param name="value" value="into"/>
132 <param name="h" value="480"/>
133 <param name="w" value="640"/>
134 <param name="mzdec" value="2"/>
135 <param name="sortpval" value="False"/>
136 <param name="tabular2" value="zip"/>
137 <param name="png2" value="zip"/>
138 </conditional>
139 </section>
140 <expand macro="test_peaklist"/>
141 </xml>
142
143 <xml name="test_annotate_quick_false">
144 <param name="quick" value="FALSE"/>
145 <section name="groupcorr">
146 <param name="cor_eic_th" value="0.75"/>
147 <param name="graphMethod" value="hcs"/>
148 <param name="pval" value="0.05"/>
149 <param name="calcCiS" value="True"/>
150 <param name="calcIso" value="False"/>
151 <param name="calcCaS" value="False"/>
152 </section>
153 </xml>
154
155 <xml name="test_annotate_quick_true">
156 <conditional name="quick_block">
157 <param name="quick" value="TRUE"/>
158 </conditional>
159 </xml>
160
161 <token name="@HELP_AUTHORS@">
162 .. class:: infomark
163
164 **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
165
166 .. class:: infomark
167
168 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
169
170 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
171
172 ---------------------------------------------------
173
174 </token>
175
176 <token name="@HELP_CAMERA_SUITE@">
177 **Version 0.1.0+camera1.48.0 - 06/11/2024**
178
179 - Initial release with core functionalities for peak annotation, grouping, and visualization using CAMERA (see CAMERA News_).
180 </token>
181
182 <token name="@HELP_CAMERA_NEWVERSION_1480@">
183 **Version 2.2.6+camera1.48.0 - 11/06/2021**
184
185 - UPGRADE: upgrade the CAMERA version from 1.46.0 to 1.48.0 (see CAMERA News_)
186 </token>
187
188 <token name="@HELP_CAMERA_NEWVERSION_1460@">
189 **Version 2.2.6+camera1.46.0 - 12/04/2021**
190
191 - UPGRADE: upgrade the CAMERA version from 1.42.0 to 1.46.0 (see CAMERA News_)
192 </token>
193
194 <token name="@HELP_CAMERA_NEWVERSION_1420@">
195 **Version 2.2.6+camera1.42.0 - 13/02/2020**
196
197 - UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0 (see CAMERA News_)
198 </token>
199
200 <xml name="citation">
201 <citations>
202 <citation type="doi">10.1021/ac202450g</citation>
203 <citation type="doi">10.1093/bioinformatics/btu813</citation>
204 </citations>
205 </xml>
206
207 <xml name="creator">
208 <creator>
209 <organization name="MELISA" url="https://www.laberca.org/plateforme-melisa/presentation"></organization>
210 <organization name="Workflow4metabolomics" url="https://workflow4metabolomics.org/"></organization>
211
212 <person givenName="Yann" familyName="Guitton" url="https://github.com/yguitton"></person>
213 <person givenName="Damien" familyName="Rat" url="https://github.com/DamienCode404"></person>
214 <person givenName="Julien" familyName="Saint-Vanne" url="https://github.com/jsaintvanne"></person>
215 </creator>
216 </xml>
217 </macros>