Mercurial > repos > bgruening > hicexplorer_chicplotviewpoint
diff chicPlotViewpoint.xml @ 2:136ebddd6ec3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
| author | iuc |
|---|---|
| date | Wed, 11 Mar 2020 17:14:05 -0400 |
| parents | ae8bf5420df2 |
| children | dbf82dd7bdb3 |
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--- a/chicPlotViewpoint.xml Wed Feb 05 19:55:06 2020 -0500 +++ b/chicPlotViewpoint.xml Wed Mar 11 17:14:05 2020 -0400 @@ -13,7 +13,7 @@ mkdir significantFolder && mkdir plots && - + #for $file in $interactionFiles: #set identifier = @ESCAPE_IDENTIFIER_FILE@ ln -s '$file' 'interactionFiles/$identifier' && @@ -37,7 +37,7 @@ #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $differentialFiles ]) #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $significantFiles ]) - + #end if @BINARY@ @@ -48,7 +48,7 @@ #end if #if $significantFiles: - --significantInteractions $significantfileslist + --significantInteractions $significantfileslist #end if -o out_plot.$image_file_format @@ -79,7 +79,7 @@ #if $dpi: --dpi $dpi - #end if + #end if #if $maxPValue: --maxPValue $maxPValue @@ -109,26 +109,26 @@ <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> <param name='differentialFiles' type="data" format="interval" label="Rejected H0 files" multiple="true" optional='true'/> <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='true'/> - + <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' /> - <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' /> + <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' /> <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" optional='true'/> - + <conditional name="batchmode_conditional"> <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> <option value="optionBatchmode">Batch processing</option> <option value="optionSinglemode" selected="True">Single file processing</option> </param> <when value="optionBatchmode"> - <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/> + <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/> <param name='differentialFilesOrderFile' type="data" format="txt" label="Rejected H0 file order" optional='true'/> <param name='significantInteractionFilesOrderFile' type="data" format="txt" label="Significant file order" optional='true'/> - <param name='computeSampleNumber' type="integer" value='2' label="Plot n sample in one plot"/> + <param name='computeSampleNumber' type="integer" value='2' label="Plot n sample in one plot"/> </when> - <when value="optionSinglemode"> + <when value="optionSinglemode"> </when> </conditional> @@ -149,21 +149,21 @@ <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> <param name='colorList' type='text' value='g b c m y k' label='Color list' help='Colorlist for the viewpoint lines. For all available colors please check matplotlib documentation: https://matplotlib.org/3.1.0/gallery/color/named_colors.html' optional='true'/> - + </inputs> <outputs> <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots"> <discover_datasets pattern="__name_and_ext__" directory="plots" /> </collection> - + </outputs> <tests> <test> - <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed"/> - <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed"/> - <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed"/> + <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt"/> + <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt"/> + <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt"/> - + <conditional name="batchmode_conditional"> <param name="batchmode_selector" value='optionBatchmode'/> <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> @@ -173,7 +173,7 @@ </conditional> <param name="pvalue" value='True'/> <param name="alpha" value='0.5'/> - <param name='backgroundModelFile' value='cHi-C/background.bed'/> + <param name='backgroundModelFile' value='cHi-C/background.txt'/> <param name='xFold' value='1.5'/> <output_collection name="plotsCollection" type="list" count="3"> <element name="Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280" file="cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png" ftype="png" compare='sim_size' delta='40000'/> @@ -183,8 +183,8 @@ </test> <test> - <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed"/> - + <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/> + <conditional name="batchmode_conditional"> <param name="batchmode_selector" value='optionSinglemode'/> </conditional> @@ -200,16 +200,16 @@ Plot of viewpoints ================== -chicPlotViewpoint plots one or many viewpoints with the average background model and the computed p-value per sample. Moreover it can highlight differential interactions of two samples and or significant regions. +chicPlotViewpoint plots one or many viewpoints with the average background model and the computed p-value per sample. Moreover it can highlight differential interactions of two samples and/or significant regions. An example usage is: -`$ chicPlotViewpoint --interactionFile viewpoint1.bed viewpoint2.bed --range 500000 500000 --backgroundModelFile background_model.bed --pValue --outFileName viewpoint1_2.png --dpi 300` +`$ chicPlotViewpoint --interactionFile viewpoint1.txt viewpoint2.txt --range 500000 500000 --backgroundModelFile background_model.txt --pValue --outFileName viewpoint1_2.png --dpi 300` In batch mode the list of file names and the folders containing the files need to be given: -`$ chicPlotViewpoint --interactionFile viewpoint_names.txt -interactionFileFolder viewpointFilesFolder --differentialTestResult rejected_H0.txt --differentialTestResultsFolder differentialFolder --range 500000 500000 --backgroundModelFile background_model.bed --pValue --outputFolder plotsFOlder --dpi 300 --threads 20` +`$ chicPlotViewpoint --interactionFile viewpoint_names.txt -interactionFileFolder viewpointFilesFolder --differentialTestResult rejected_H0.txt --differentialTestResultsFolder differentialFolder --range 500000 500000 --backgroundModelFile background_model.txt --pValue --outputFolder plotsFOlder --dpi 300 --threads 20` For more information about HiCExplorer please consider our documentation on readthedocs.io_