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comparison abims_CAMERA_annotateDiffreport.xml @ 18:cb923396e70f draft

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planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
author lecorguille
date Thu, 29 Aug 2019 11:38:21 -0400
parents 73d82de36369
children 01459b73daf9
comparison
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17:73d82de36369 18:cb923396e70f
1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.4"> 1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.5">
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 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
8 8
9 <expand macro="requirements"/> 9 <expand macro="requirements"/>
10 <expand macro="stdio"/> 10 <expand macro="stdio"/>
11 11
12 <command><![CDATA[ 12 <command><![CDATA[
13 @COMMAND_CAMERA_SCRIPT@ 13 @COMMAND_RSCRIPT@/CAMERA_annotateDiffreport.r
14 xfunction annotatediff
15 image '$image' 14 image '$image'
16 15
17 nSlaves \${GALAXY_SLOTS:-1} 16 nSlaves \${GALAXY_SLOTS:-1}
18
19 ## output
20 variableMetadataOutput '$variableMetadata'
21 17
22 ## groupFWHM 18 ## groupFWHM
23 sigma $groupfwhm.sigma 19 sigma $groupfwhm.sigma
24 perfwhm $groupfwhm.perfwhm 20 perfwhm $groupfwhm.perfwhm
25 21
32 maxiso $findisotopes.maxiso 28 maxiso $findisotopes.maxiso
33 minfrac $findisotopes.minfrac 29 minfrac $findisotopes.minfrac
34 30
35 quick $quick_block.quick 31 quick $quick_block.quick
36 #if $quick_block.quick == "FALSE": 32 #if $quick_block.quick == "FALSE":
37 xsetRdataOutput '$rdata_quick_false'
38
39 ## groupcorr 33 ## groupcorr
40 cor_eic_th $quick_block.groupcorr.cor_eic_th 34 cor_eic_th $quick_block.groupcorr.cor_eic_th
41 graphMethod $quick_block.groupcorr.graphMethod 35 graphMethod $quick_block.groupcorr.graphMethod
42 pval $quick_block.groupcorr.pval 36 pval $quick_block.groupcorr.pval
43 calcCiS $quick_block.groupcorr.calcCiS 37 calcCiS $quick_block.groupcorr.calcCiS
50 #if $quick_block.findadducts.rules_block.rules_select == "FALSE": 44 #if $quick_block.findadducts.rules_block.rules_select == "FALSE":
51 multiplier $quick_block.findadducts.rules_block.multiplier 45 multiplier $quick_block.findadducts.rules_block.multiplier
52 #else 46 #else
53 rules $quick_block.findadducts.rules_block.rules 47 rules $quick_block.findadducts.rules_block.rules
54 #end if 48 #end if
55 #else
56 xsetRdataOutput '$rdata_quick_true'
57 #end if 49 #end if
58 50
59 #if $diffreport.options.option == "show": 51 #if $diffreport.options.option == "show":
60 ## diffreport 52 ## diffreport
61 runDiffreport TRUE 53 runDiffreport TRUE
64 value $diffreport.options.value 56 value $diffreport.options.value
65 sortpval $diffreport.options.sortpval 57 sortpval $diffreport.options.sortpval
66 h $diffreport.options.h 58 h $diffreport.options.h
67 w $diffreport.options.w 59 w $diffreport.options.w
68 mzdec $diffreport.options.mzdec 60 mzdec $diffreport.options.mzdec
61 tabular2 $diffreport.options.tabular2
62 png2 $diffreport.options.png2
69 #end if 63 #end if
70 64
71 @COMMAND_PEAKLIST@ 65 @COMMAND_PEAKLIST@
72 66
73 @COMMAND_FILE_LOAD@ 67 @COMMAND_FILE_LOAD@
157 </param> 151 </param>
158 <param name="h" type="integer" value="480" label="Numeric variable for the height of the eic and boxplots that are printed out" help="[height]" /> 152 <param name="h" type="integer" value="480" label="Numeric variable for the height of the eic and boxplots that are printed out" help="[height]" />
159 <param name="w" type="integer" value="640" label="Numeric variable for the width of the eic and boxplots print out made" help="[width]" /> 153 <param name="w" type="integer" value="640" label="Numeric variable for the width of the eic and boxplots print out made" help="[width]" />
160 <param name="mzdec" type="integer" value="2" label="Number of decimal places of title m/z values in the eic plot" help="[mzdec]" /> 154 <param name="mzdec" type="integer" value="2" label="Number of decimal places of title m/z values in the eic plot" help="[mzdec]" />
161 <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/> 155 <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/>
156 <param name="tabular2" type="select" label="Export the Diffreport files in ">
157 <option value="zip" selected="true">Zip</option>
158 <option value="datasetcollection">Individual file in a Dataset Collection</option>
159 </param>
160 <param name="png2" type="select" label="Export the EIC and boxplots in ">
161 <option value="zip" selected="true">Zip</option>
162 <option value="pdf">Individual pdf</option>
163 </param>
162 </when> 164 </when>
163 <when value="hide"> 165 <when value="hide">
164 </when> 166 </when>
165 </conditional> 167 </conditional>
166 </section> 168 </section>
168 <expand macro="input_peaklist"/> 170 <expand macro="input_peaklist"/>
169 <expand macro="input_file_load"/> 171 <expand macro="input_file_load"/>
170 </inputs> 172 </inputs>
171 173
172 <outputs> 174 <outputs>
173 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" /> 175 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
174 <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" > 176 <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" from_work_dir="annotatediff.RData">
175 <filter>quick_block['quick'] == 'FALSE'</filter> 177 <filter>quick_block['quick'] == 'FALSE'</filter>
176 <change_format> 178 <change_format>
177 <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" /> 179 <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" />
178 <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" /> 180 <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" />
179 </change_format> 181 </change_format>
180 </data> 182 </data>
181 <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" > 183 <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" from_work_dir="annotatediff.RData">
182 <filter>quick_block['quick'] == 'TRUE'</filter> 184 <filter>quick_block['quick'] == 'TRUE'</filter>
183 </data> 185 </data>
184 <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="true"> 186
185 <filter>diffreport['options']['option'] == 'show'</filter> 187 <data name="output_diffreport_eic_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_eic.zip" from_work_dir="eic.zip" >
186 <discover_datasets pattern="__designation_and_ext__" directory="pdf" visible="true" /> 188 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'zip'</filter>
187 <discover_datasets pattern="__designation_and_ext__" directory="tabular" visible="true" />
188 </data> 189 </data>
190 <data name="output_diffreport_box_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_box.zip" from_work_dir="box.zip" >
191 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'zip'</filter>
192 </data>
193 <collection name="output_diffreport_picture_pdf" type="list" label="${image.name[:-6]}.annotateDiffreport.pdf">
194 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'pdf'</filter>
195 <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" />
196 </collection>
197
198 <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_table.zip" from_work_dir="tabular.zip">
199 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'zip'</filter>
200 </data>
201 <collection name="output_diffreport_table_collection" type="list" label="${image.name[:-6]}.annotateDiffreport_table">
202 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'datasetcollection'</filter>
203 <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular" />
204 </collection>
189 </outputs> 205 </outputs>
190 206
191 <tests> 207 <tests>
192 <!--<test> 208 <!--<test>
193 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/> 209 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/>
416 --------------------------------------------------- 432 ---------------------------------------------------
417 433
418 Changelog/News 434 Changelog/News
419 -------------- 435 --------------
420 436
437 .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
438
439 **Version 2.2.5 - 09/04/2019**
440
441 - NEW: zip export are back for pictures (eic and boxplot) and diffreport tables
442
443 - UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)
444
445 - UPGRADE: refactoring of internal code
446
421 **Version 2.2.4 - 09/10/2018** 447 **Version 2.2.4 - 09/10/2018**
422 448
423 - NES: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job 449 - NEW: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job
424 450
425 **Version 2.2.3 - 30/04/2018** 451 **Version 2.2.3 - 30/04/2018**
426 452
427 - NEW: support the new xcms 3.0.0 wrapper 453 - NEW: support the new xcms 3.0.0 wrapper
428 454