Mercurial > repos > lecorguille > camera_annotate
diff abims_CAMERA_annotateDiffreport.xml @ 18:cb923396e70f draft
planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
author | lecorguille |
---|---|
date | Thu, 29 Aug 2019 11:38:21 -0400 |
parents | 73d82de36369 |
children | 01459b73daf9 |
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--- a/abims_CAMERA_annotateDiffreport.xml Tue Oct 09 06:03:01 2018 -0400 +++ b/abims_CAMERA_annotateDiffreport.xml Thu Aug 29 11:38:21 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.4"> +<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.5"> <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> @@ -10,15 +10,11 @@ <expand macro="stdio"/> <command><![CDATA[ - @COMMAND_CAMERA_SCRIPT@ - xfunction annotatediff + @COMMAND_RSCRIPT@/CAMERA_annotateDiffreport.r image '$image' nSlaves \${GALAXY_SLOTS:-1} - ## output - variableMetadataOutput '$variableMetadata' - ## groupFWHM sigma $groupfwhm.sigma perfwhm $groupfwhm.perfwhm @@ -34,8 +30,6 @@ quick $quick_block.quick #if $quick_block.quick == "FALSE": - xsetRdataOutput '$rdata_quick_false' - ## groupcorr cor_eic_th $quick_block.groupcorr.cor_eic_th graphMethod $quick_block.groupcorr.graphMethod @@ -52,8 +46,6 @@ #else rules $quick_block.findadducts.rules_block.rules #end if - #else - xsetRdataOutput '$rdata_quick_true' #end if #if $diffreport.options.option == "show": @@ -66,6 +58,8 @@ h $diffreport.options.h w $diffreport.options.w mzdec $diffreport.options.mzdec + tabular2 $diffreport.options.tabular2 + png2 $diffreport.options.png2 #end if @COMMAND_PEAKLIST@ @@ -159,6 +153,14 @@ <param name="w" type="integer" value="640" label="Numeric variable for the width of the eic and boxplots print out made" help="[width]" /> <param name="mzdec" type="integer" value="2" label="Number of decimal places of title m/z values in the eic plot" help="[mzdec]" /> <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/> + <param name="tabular2" type="select" label="Export the Diffreport files in "> + <option value="zip" selected="true">Zip</option> + <option value="datasetcollection">Individual file in a Dataset Collection</option> + </param> + <param name="png2" type="select" label="Export the EIC and boxplots in "> + <option value="zip" selected="true">Zip</option> + <option value="pdf">Individual pdf</option> + </param> </when> <when value="hide"> </when> @@ -170,22 +172,36 @@ </inputs> <outputs> - <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" /> - <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" > + <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" /> + <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" from_work_dir="annotatediff.RData"> <filter>quick_block['quick'] == 'FALSE'</filter> <change_format> <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" /> <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" /> </change_format> </data> - <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" > + <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" from_work_dir="annotatediff.RData"> <filter>quick_block['quick'] == 'TRUE'</filter> </data> - <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="true"> - <filter>diffreport['options']['option'] == 'show'</filter> - <discover_datasets pattern="__designation_and_ext__" directory="pdf" visible="true" /> - <discover_datasets pattern="__designation_and_ext__" directory="tabular" visible="true" /> + + <data name="output_diffreport_eic_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_eic.zip" from_work_dir="eic.zip" > + <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'zip'</filter> + </data> + <data name="output_diffreport_box_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_box.zip" from_work_dir="box.zip" > + <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'zip'</filter> </data> + <collection name="output_diffreport_picture_pdf" type="list" label="${image.name[:-6]}.annotateDiffreport.pdf"> + <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'pdf'</filter> + <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" /> + </collection> + + <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_table.zip" from_work_dir="tabular.zip"> + <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'zip'</filter> + </data> + <collection name="output_diffreport_table_collection" type="list" label="${image.name[:-6]}.annotateDiffreport_table"> + <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'datasetcollection'</filter> + <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular" /> + </collection> </outputs> <tests> @@ -418,9 +434,19 @@ Changelog/News -------------- +.. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS + +**Version 2.2.5 - 09/04/2019** + +- NEW: zip export are back for pictures (eic and boxplot) and diffreport tables + +- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_) + +- UPGRADE: refactoring of internal code + **Version 2.2.4 - 09/10/2018** -- NES: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job +- NEW: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job **Version 2.2.3 - 30/04/2018**