Mercurial > repos > lecorguille > camera_annotate

comparison abims_CAMERA_annotateDiffreport.xml @ 9:7da9252dd983 draft

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planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
author lecorguille
date Mon, 25 Apr 2016 11:06:25 -0400
parents 8c5bb7b86df9
children 8dd6f0ffa763
comparison
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8:8c5bb7b86df9 9:7da9252dd983
1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.3"> 1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.5">
2 2
3 <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> 3 <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
4 4
5 <requirements> 5 <macros>
6 <requirement type="package" version="3.1.2">R</requirement> 6 <import>macros.xml</import>
7 <requirement type="binary">Rscript</requirement> 7 </macros>
8 <requirement type="package" version="1.44.0">xcms</requirement> 8
9 <requirement type="package" version="1.22.0">camera</requirement> 9 <expand macro="requirements"/>
10 <requirement type="package" version="2.2.1">camera_w4m_script</requirement> 10 <expand macro="stdio"/>
11 <requirement type="binary">CAMERA.r</requirement>
12 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
13 <requirement type="binary">convert</requirement>
14 </requirements>
15
16 <stdio>
17 <exit_code range="1:" level="fatal" />
18 </stdio>
19 11
20 <command><![CDATA[ 12 <command><![CDATA[
21 CAMERA.r 13 @COMMAND_CAMERA_SCRIPT@
22 xfunction annotatediff 14 xfunction annotatediff
23 image $image 15 image $image
24 16
25 variableMetadataOutput $variableMetadata 17 variableMetadataOutput $variableMetadata
26 dataMatrixOutput $datamatrix 18 dataMatrixOutput $datamatrix
54 w $options.w 46 w $options.w
55 mzdec $options.mzdec 47 mzdec $options.mzdec
56 new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_ 48 new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
57 #end if 49 #end if
58 50
59 51 #if $zip_file:
52 zipfile $zip_file
53 #end if
54
60 ]]></command> 55 ]]></command>
61 56
62 <inputs> 57 <inputs>
63 58
64 59
129 <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="diffreport: logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/> 124 <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="diffreport: logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/>
130 </when> 125 </when>
131 <when value="hide"> 126 <when value="hide">
132 </when> 127 </when>
133 </conditional> 128 </conditional>
134 129
130 <!-- To pass planemo test -->
131 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." />
135 </inputs> 132 </inputs>
136 133
137 <outputs> 134 <outputs>
138 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" /> 135 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" />
139 <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" /> 136 <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" />
141 <change_format> 138 <change_format>
142 <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" /> 139 <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" />
143 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" /> 140 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" />
144 </change_format> 141 </change_format>
145 </data> 142 </data>
146 <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True"> 143 <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True">
147 <filter>(options['option'] == 'show')</filter> 144 <filter>(options['option'] == 'show')</filter>
148 </data> 145 </data>
149 </outputs> 146 </outputs>
150 147
151 <tests> 148 <tests>
152 <test> 149 <!--<test>
153 <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/> 150 <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/>
154 <param name="convert_param" value="False"/> 151 <param name="convert_param" value="False"/>
155 <param name="num_digits" value="0"/> 152 <param name="num_digits" value="0"/>
156 <param name="sigma" value="6"/> 153 <param name="sigma" value="6"/>
157 <param name="perfwhm" value="0.6"/> 154 <param name="perfwhm" value="0.6"/>
160 <param name="minfrac" value="0.5"/> 157 <param name="minfrac" value="0.5"/>
161 <param name="ppm" value="5"/> 158 <param name="ppm" value="5"/>
162 <param name="mzabs" value="0.015"/> 159 <param name="mzabs" value="0.015"/>
163 <param name="intval" value="into"/> 160 <param name="intval" value="into"/>
164 <param name="max_peaks" value="100"/> 161 <param name="max_peaks" value="100"/>
165 <param name="quick_block.quick" value="FALSE"/> 162 <param name="quick_block|quick" value="FALSE"/>
166 <param name="quick_block.polarity" value="negative"/> 163 <param name="quick_block|polarity" value="negative"/>
167 <param name="quick_block.cor_eic_th" value="0.75"/> 164 <param name="quick_block|cor_eic_th" value="0.75"/>
168 <param name="quick_block.graphMethod" value="hcs"/> 165 <param name="quick_block|graphMethod" value="hcs"/>
169 <param name="quick_block.pval" value="0.05"/> 166 <param name="quick_block|pval" value="0.05"/>
170 <param name="quick_block.calcCiS" value="True"/> 167 <param name="quick_block|calcCiS" value="True"/>
171 <param name="quick_block.calcIso" value="False"/> 168 <param name="quick_block|calcIso" value="False"/>
172 <param name="quick_block.calcCaS" value="False"/> 169 <param name="quick_block|calcCaS" value="False"/>
173 <param name="quick_block.multiplier" value="3"/> 170 <param name="quick_block|multiplier" value="3"/>
174 <param name="options.option" value="show"/> 171 <param name="options|option" value="show"/>
175 <param name="options.eicmax" value="200"/> 172 <param name="options|eicmax" value="200"/>
176 <param name="options.eicwidth" value="200"/> 173 <param name="options|eicwidth" value="200"/>
177 <param name="options.value" value="into"/> 174 <param name="options|value" value="into"/>
178 <param name="options.h" value="480"/> 175 <param name="options|h" value="480"/>
179 <param name="options.w" value="640"/> 176 <param name="options|w" value="640"/>
180 <param name="options.mzdec" value="2"/> 177 <param name="options|mzdec" value="2"/>
181 <param name="options.sortpval" value="False"/> 178 <param name="options|sortpval" value="False"/>
179 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" />
182 <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> 180 <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
183 <output name="datamatrix" file="xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> 181 <output name="datamatrix" file="xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
184 <output name="rdata" file="xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> 182 </test>-->
183 <test>
184 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/>
185 <param name="convert_param" value="False"/>
186 <param name="num_digits" value="0"/>
187 <param name="sigma" value="6"/>
188 <param name="perfwhm" value="0.6"/>
189 <param name="maxcharge" value="3"/>
190 <param name="maxiso" value="4"/>
191 <param name="minfrac" value="0.5"/>
192 <param name="ppm" value="5"/>
193 <param name="mzabs" value="0.015"/>
194 <param name="intval" value="into"/>
195 <param name="max_peaks" value="100"/>
196 <param name="quick_block|quick" value="FALSE"/>
197 <param name="quick_block|polarity" value="negative"/>
198 <param name="quick_block|cor_eic_th" value="0.75"/>
199 <param name="quick_block|graphMethod" value="hcs"/>
200 <param name="quick_block|pval" value="0.05"/>
201 <param name="quick_block|calcCiS" value="True"/>
202 <param name="quick_block|calcIso" value="False"/>
203 <param name="quick_block|calcCaS" value="False"/>
204 <param name="quick_block|multiplier" value="3"/>
205 <param name="options|option" value="show"/>
206 <param name="options|eicmax" value="200"/>
207 <param name="options|eicwidth" value="200"/>
208 <param name="options|value" value="into"/>
209 <param name="options|h" value="480"/>
210 <param name="options|w" value="640"/>
211 <param name="options|mzdec" value="2"/>
212 <param name="options|sortpval" value="False"/>
213 <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" />
214 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
215 <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
185 </test> 216 </test>
186 </tests> 217 </tests>
187 218
188 219
189 220
190 <help><![CDATA[ 221 <help><![CDATA[
191 222
192 .. class:: infomark 223 @HELP_AUTHORS@
193
194 **Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de
195
196 .. class:: infomark
197
198 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]
199
200 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
201
202 ---------------------------------------------------
203
204 224
205 ================ 225 ================
206 CAMERA.annotate 226 CAMERA.annotate
207 ================ 227 ================
208 228
376 --------------------------------------------------- 396 ---------------------------------------------------
377 397
378 Changelog/News 398 Changelog/News
379 -------------- 399 --------------
380 400
381 **Version 2.1.3 - 10/02/2016** 401 **Version 2.1.5 - 21/04/2016**
402
403 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0
404
405
406 **Version 2.1.4 - 18/04/2016**
407
408 - TEST: refactoring to pass planemo test using conda dependencies
409
410
411 **Version 2.1.3 - 10/02/2016**
382 412
383 - BUGFIX: better management of errors. Datasets remained green although the process failed 413 - BUGFIX: better management of errors. Datasets remained green although the process failed
384 414
385 - BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions) 415 - BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions)
386 416
403 - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions 433 - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions
404 434
405 435
406 ]]></help> 436 ]]></help>
407 437
408 <citations> 438 <expand macro="citation" />
409 <citation type="doi">10.1021/ac202450g</citation>
410 <citation type="doi">10.1093/bioinformatics/btu813</citation>
411 </citations>
412 439
413 440
414 </tool> 441 </tool>
415 442
416 443