Mercurial > repos > lecorguille > camera_annotate
diff abims_CAMERA_annotateDiffreport.xml @ 36:b6a8143c397c draft
planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
| author | lecorguille |
|---|---|
| date | Fri, 01 Feb 2019 11:29:35 -0500 |
| parents | b02797fbead1 |
| children | 636e36a64d31 |
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--- a/abims_CAMERA_annotateDiffreport.xml Fri Aug 17 06:45:55 2018 -0400 +++ b/abims_CAMERA_annotateDiffreport.xml Fri Feb 01 11:29:35 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.3"> +<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> @@ -18,7 +18,6 @@ ## output variableMetadataOutput '$variableMetadata' - dataMatrixOutput '$datamatrix' ## groupFWHM sigma $groupfwhm.sigma @@ -67,6 +66,8 @@ h $diffreport.options.h w $diffreport.options.w mzdec $diffreport.options.mzdec + tabular2 $diffreport.options.tabular2 + png2 $diffreport.options.png2 #end if @COMMAND_PEAKLIST@ @@ -160,6 +161,14 @@ <param name="w" type="integer" value="640" label="Numeric variable for the width of the eic and boxplots print out made" help="[width]" /> <param name="mzdec" type="integer" value="2" label="Number of decimal places of title m/z values in the eic plot" help="[mzdec]" /> <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/> + <param name="tabular2" type="select" label="Export the Diffreport files in "> + <option value="zip" selected="true">Zip</option> + <option value="datasetcollection">Individual file in a Dataset Collection</option> + </param> + <param name="png2" type="select" label="Export the EIC and boxplots in "> + <option value="zip" selected="true">Zip</option> + <option value="pdf">Individual pdf</option> + </param> </when> <when value="hide"> </when> @@ -172,7 +181,6 @@ <outputs> <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" /> - <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" /> <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" > <filter>quick_block['quick'] == 'FALSE'</filter> <change_format> @@ -183,11 +191,25 @@ <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" > <filter>quick_block['quick'] == 'TRUE'</filter> </data> - <data name="output_diffreport" format="text" label="${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="${image.name[:-6]}.annotateDiffreport.pdf"> + <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'pdf'</filter> + <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" visible="true" /> + </collection> + + <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport.pdf" 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" visible="true" /> + </collection> </outputs> <tests> @@ -197,23 +219,20 @@ <expand macro="test_annotate_quick_true"/> <expand macro="test_file_load_zip"/> <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> - <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> </test>--> <test> <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/> <expand macro="test_annotate_diffreport"/> <expand macro="test_annotate_quick_true"/> <expand macro="test_file_load_single"/> - <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> - <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> + <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" lines_diff="2" /> </test> <test> <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks-xcms3.RData"/> <expand macro="test_annotate_diffreport"/> <expand macro="test_annotate_quick_true"/> <expand macro="test_file_load_single"/> - <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata-xcms3.tsv" /> - <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix-xcms3.tsv" /> + <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata-xcms3.tsv" lines_diff="2" /> </test> <test> <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/> @@ -229,8 +248,7 @@ </section> </conditional> <expand macro="test_file_load_single"/> - <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" /> - <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv" /> + <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" lines_diff="2"/> </test> </tests> @@ -287,19 +305,19 @@ +===========================+=======================================+================================================+ |CAMERA_combinexsAnnot |xset.annotate.Rdata | rdata.camera.positive or rdata.camera.negative | +---------------------------+---------------------------------------+------------------------------------------------+ -|Determine Vdk or Lowess |xset.annotate.dataMatrix.tsv | Tabular | +|Determine Vdk or Lowess |xset.annotate.variableMetadata.tsv | Tabular | +---------------------------+---------------------------------------+------------------------------------------------+ -|Normalization Vdk/Lowess |xset.annotate.dataMatrix.tsv | Tabular | +|Normalization Vdk/Lowess |xset.annotate.variableMetadata.tsv | Tabular | +---------------------------+---------------------------------------+------------------------------------------------+ -|Anova |xset.annotate.dataMatrix.tsv | Tabular | +|Anova |xset.annotate.variableMetadata.tsv | Tabular | +---------------------------+---------------------------------------+------------------------------------------------+ -|PCA |xset.annotate.dataMatrix.tsv | Tabular | +|PCA |xset.annotate.variableMetadata.tsv | Tabular | +---------------------------+---------------------------------------+------------------------------------------------+ -|Hierarchical Clustering |xset.annotate.dataMatrix.tsv | Tabular | +|Hierarchical Clustering |xset.annotate.variableMetadata.tsv | Tabular | +---------------------------+---------------------------------------+------------------------------------------------+ -The output file **xset.annotate.dataMatrix.tsv** is an tabular file. You can continue your analysis using it in the following tools: +The output file **xset.annotate.variableMetadata.tsv** is an tabular file. You can continue your analysis using it in the following tools: | Determine Vdk or Lowess | Normalization Vdk/Lowess @@ -361,10 +379,6 @@ | For each metabolite (row) : | the value of the intensity in each sample, fold, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct and pcgroup -xset.annotate.dataMatrix.tsv - - | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column). - xset.annotate.zip | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis). @@ -377,7 +391,7 @@ .. class:: infomark -The output **"xset.annotate.dataMatrix.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow: +The output **"xset.annotate.variableMetadata.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow: | Determine Vdk or Lowess (Data correction) | Normalization Vdk/Lowess (Data correction) @@ -418,10 +432,6 @@ Output files ------------ -**Example of an xset.annotate.dataMatrix.tsv output** - -.. image:: annotatediffreport_dataMatrix.png - **Example of a part of xset.annotate.variableMetadata.tsv output** .. image:: annotatediffreport_variableMetadata.png @@ -432,6 +442,14 @@ Changelog/News -------------- +**Version 2.2.5 - 01/02/2019** + +- NEW: zip export are back for pictures (eic and boxplot) and diffreport tables + +**Version 2.2.4 - 09/10/2018** + +- NEW: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job + **Version 2.2.3 - 30/04/2018** - NEW: support the new xcms 3.0.0 wrapper