Mercurial > repos > workflow4metabolomics > camera_combinexsannos

comparison macros.xml @ 7:e461f344226c draft default tip

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planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d
author workflow4metabolomics
date Sun, 24 Nov 2024 21:28:22 +0000
parents 2443150161b4
children
comparison
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6:2443150161b4 7:e461f344226c
35 </token> 35 </token>
36 36
37 <xml name="input_file_load"> 37 <xml name="input_file_load">
38 <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> 38 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
39 <conditional name="file_load_conditional"> 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." > 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> 41 <option value="no">no need</option>
42 <option value="yes" >yes</option> 42 <option value="yes">yes</option>
43 </param> 43 </param>
44 <when value="no"> 44 <when value="no">
45 </when> 45 </when>
46 <when value="yes"> 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." /> 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." />
62 <xml name="test_file_load_single"> 62 <xml name="test_file_load_single">
63 <section name="file_load_section"> 63 <section name="file_load_section">
64 <conditional name="file_load_conditional"> 64 <conditional name="file_load_conditional">
65 <param name="file_load_select" value="yes" /> 65 <param name="file_load_select" value="yes" />
66 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> 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" />
67 </conditional> 76 </conditional>
68 </section> 77 </section>
69 </xml> 78 </xml>
70 79
71 <!-- peaklist export option management --> 80 <!-- peaklist export option management -->
81 <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"/> 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"/>
82 <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" /> 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" />
83 <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" /> 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" />
84 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below"> 93 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
85 <option value="into" selected="true">into</option> 94 <option value="into" selected="true">into</option>
86 <option value="maxo" >maxo</option> 95 <option value="maxo">maxo</option>
87 <option value="intb">intb</option> 96 <option value="intb">intb</option>
88 </param> 97 </param>
89 </section> 98 </section>
90 </xml> 99 </xml>
91 100
113 <param name="ppm" value="5"/> 122 <param name="ppm" value="5"/>
114 <param name="mzabs" value="0.015"/> 123 <param name="mzabs" value="0.015"/>
115 <param name="max_peaks" value="100"/> 124 <param name="max_peaks" value="100"/>
116 </section> 125 </section>
117 <section name="diffreport"> 126 <section name="diffreport">
118 <conditional name="options"> 127 <conditional name="options">
119 <param name="option" value="show"/> 128 <param name="option" value="show"/>
120 <param name="eicmax" value="200"/> 129 <param name="eicmax" value="200"/>
121 <param name="eicwidth" value="200"/> 130 <param name="eicwidth" value="200"/>
122 <param name="value" value="into"/> 131 <param name="value" value="into"/>
123 <param name="h" value="480"/> 132 <param name="h" value="480"/>
124 <param name="w" value="640"/> 133 <param name="w" value="640"/>
125 <param name="mzdec" value="2"/> 134 <param name="mzdec" value="2"/>
126 <param name="sortpval" value="False"/> 135 <param name="sortpval" value="False"/>
127 <param name="tabular2" value="zip"/> 136 <param name="tabular2" value="zip"/>
128 <param name="png2" value="zip"/> 137 <param name="png2" value="zip"/>
129 </conditional> 138 </conditional>
130 </section> 139 </section>
131 <expand macro="test_peaklist"/> 140 <expand macro="test_peaklist"/>
132 </xml> 141 </xml>
133 142
134 <xml name="test_annotate_quick_false"> 143 <xml name="test_annotate_quick_false">
162 171
163 --------------------------------------------------- 172 ---------------------------------------------------
164 173
165 </token> 174 </token>
166 175
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
167 <token name="@HELP_CAMERA_NEWVERSION_1480@"> 182 <token name="@HELP_CAMERA_NEWVERSION_1480@">
168 **Version 2.2.6+camera1.48.0 - 11/06/2021** 183 **Version 2.2.6+camera1.48.0 - 11/06/2021**
169 184
170 - UPGRADE: upgrade the CAMERA version from 1.46.0 to 1.48.0 (see CAMERA News_) 185 - UPGRADE: upgrade the CAMERA version from 1.46.0 to 1.48.0 (see CAMERA News_)
171 </token> 186 </token>
186 <citations> 201 <citations>
187 <citation type="doi">10.1021/ac202450g</citation> 202 <citation type="doi">10.1021/ac202450g</citation>
188 <citation type="doi">10.1093/bioinformatics/btu813</citation> 203 <citation type="doi">10.1093/bioinformatics/btu813</citation>
189 </citations> 204 </citations>
190 </xml> 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>
191 </macros> 217 </macros>