Mercurial > repos > bgruening > hicexplorer_chicplotviewpoint
diff chicPlotViewpoint.xml @ 6:031872f8e2e0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 14:50:31 +0000 |
| parents | ac7999229ac6 |
| children | 013e53ccc7ac |
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--- a/chicPlotViewpoint.xml Fri Dec 11 21:20:38 2020 +0000 +++ b/chicPlotViewpoint.xml Tue Mar 16 14:50:31 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1"> +<tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>creates plots for viewpoints</description> <macros> <token name="@BINARY@">chicPlotViewpoint</token> @@ -42,12 +42,10 @@ #end for #end if - #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.interactionFiles ]) #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.differentialFiles ]) #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.significantFiles ]) - #end if @BINARY@ @@ -78,13 +76,11 @@ --batchMode --outputFolder plots --outputFormat $image_file_format - - #end if --range $rangeUpstream $rangeDownstream #if $backgroundModelFile: - --backgroundModelFile $backgroundModelFile + --backgroundModelFile '$backgroundModelFile' #end if #if $dpi: @@ -121,7 +117,7 @@ && cd .. && rm -rf plots #end if - ]]></command> + ]]> </command> <inputs> <conditional name="tar_input_conditional"> <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> @@ -129,22 +125,20 @@ <option value="interval_input" selected="True">Interval files</option> </param> <when value="tar_input"> - <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/> - <param name='differentialFiles' type="data" format="tar" label="Rejected H0 files" multiple="true" optional='false'/> - <param name='significantFiles' type="data" format="tar" label="Significant interaction files" multiple="true" optional='false'/> + <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" /> + <param name='differentialFiles' type="data" format="tar" label="Rejected H0 files" multiple="true" optional='false' /> + <param name='significantFiles' type="data" format="tar" label="Significant interaction files" multiple="true" optional='false' /> </when> <when value="interval_input"> - <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='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' /> </when> </conditional> - <param name="rangeUpstream" type="integer" value="100000" 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="100000" 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'/> + <param name="rangeUpstream" type="integer" value="100000" 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="100000" 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"> @@ -152,38 +146,34 @@ <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='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='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" /> </when> <when value="optionSinglemode"> </when> </conditional> - - <param argument="--maxPValue" type="float" optional="true" label="Max p-value" help="Maximum value of the plotted p-value."/> - <param argument="--minPValue" type="float" optional="true" label="Min p-value" help="Minimum value of the plotted p-value."/> - <param name='resolution' type='integer' value='1000' label='Resolution of cHi-C data' help='Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution.' optional='true'/> - <param name='pvalue' type='boolean' truevalue='--pValue' falsevalue="" checked="false" label="Plot p-values as a colorbar"/> + <param argument="--maxPValue" type="float" optional="true" label="Max p-value" help="Maximum value of the plotted p-value." /> + <param argument="--minPValue" type="float" optional="true" label="Min p-value" help="Minimum value of the plotted p-value." /> + <param name='resolution' type='integer' value='1000' min="1" optional='true' label='Resolution of cHi-C data' help='Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution.' /> + <param name='pvalue' type='boolean' truevalue='--pValue' falsevalue="" checked="false" label="Plot p-values as a colorbar" /> <expand macro="colormap" /> - <param name='xFold' type='float' value='' label='X-fold mean background' help='Plot x-fold region for the mean background.' optional='true'/> + <param name='xFold' type='float' value='' optional='true' label='X-fold mean background' help='Plot x-fold region for the mean background.' /> <param name="image_file_format" type="select" label="Image output format"> <option value="png" selected="True">png</option> <option value="svg">svg</option> <option value="pdf">pdf</option> </param> - <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'/> - <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one." - help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not disturbing the presenation of small p-values."/> - - <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file" - help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/> - + <param name='dpi' type='integer' optional='true' label='DPI for image' help='Change the default resolution of the plot.' /> + <param name='colorList' type='text' value='g b c m y k' optional='true' label='Color list' help='Colorlist for the viewpoint lines. For all available colors please check matplotlib documentation: https://matplotlib.org/stable/gallery/color/named_colors.html'> + <validator type="expression" message="Only alphabetic characters and the colon are allowed.">value.replace(' ', '').replace(':', '').isalpha()</validator> + </param> + <param argument='--truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one." help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not disturbing the presenation of small p-values." /> + <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file" help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large." /> </inputs> <outputs> <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots"> @@ -196,109 +186,104 @@ <tests> <test> <conditional name="tar_input_conditional"> - <param name="tar_input_selector" value='interval_input'/> - <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_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt"/> + <param name="tar_input_selector" value='interval_input' /> + <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_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" /> </conditional> - - <conditional name="batchmode_conditional"> - <param name="batchmode_selector" value='optionBatchmode'/> - <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> - <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/> - <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/> - <param name='computeSampleNumber' value='2'/> + <param name="batchmode_selector" value='optionBatchmode' /> + <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> + <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt' /> + <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt' /> + <param name='computeSampleNumber' value='2' /> </conditional> - <param name="pvalue" value='True'/> - <param name="truncateZeroPvalues" value='True'/> + <param name="pvalue" value='True' /> + <param name="truncateZeroPvalues" value='True' /> - <param name='backgroundModelFile' value='cHi-C/background.txt'/> - <param name='xFold' value='1.5'/> + <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'/> - <element name="Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435" file="cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png" ftype="png" compare='sim_size' delta='40000'/> - <element name="Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103" file="cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png" ftype="png" compare='sim_size' delta='40000'/> + <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' /> + <element name="Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435" file="cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png" ftype="png" compare='sim_size' /> + <element name="Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103" file="cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png" ftype="png" compare='sim_size' /> </output_collection> - </test> <test> <conditional name="tar_input_conditional"> - <param name="tar_input_selector" value='interval_input'/> - <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/> + <param name="tar_input_selector" value='interval_input' /> + <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" /> </conditional> <conditional name="batchmode_conditional"> - <param name="batchmode_selector" value='optionSinglemode'/> + <param name="batchmode_selector" value='optionSinglemode' /> </conditional> <output_collection name="plotsCollection" type="list" count="1"> - <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/> - + <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' /> </output_collection> </test> <test> <conditional name="tar_input_conditional"> - <param name="tar_input_selector" value='interval_input'/> - <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/> + <param name="tar_input_selector" value='interval_input' /> + <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" /> </conditional> <conditional name="batchmode_conditional"> - <param name="batchmode_selector" value='optionSinglemode'/> + <param name="batchmode_selector" value='optionSinglemode' /> </conditional> <output_collection name="plotsCollection" type="list" count="1"> - <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/> - + <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' /> </output_collection> </test> <test> <conditional name="tar_input_conditional"> - <param name="tar_input_selector" value='interval_input'/> - <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_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt"/> + <param name="tar_input_selector" value='interval_input' /> + <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_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" /> </conditional> <conditional name="batchmode_conditional"> - <param name="batchmode_selector" value='optionBatchmode'/> - <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> - <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/> - <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/> - <param name='computeSampleNumber' value='2'/> + <param name="batchmode_selector" value='optionBatchmode' /> + <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> + <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt' /> + <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt' /> + <param name='computeSampleNumber' value='2' /> </conditional> - <param name="pvalue" value='True'/> - <param name="truncateZeroPvalues" value='True'/> + <param name="pvalue" value='True' /> + <param name="truncateZeroPvalues" value='True' /> - <param name='backgroundModelFile' value='cHi-C/background.txt'/> - <param name='xFold' value='1.5'/> - <param name='tar' value='True'/> + <param name='backgroundModelFile' value='cHi-C/background.txt' /> + <param name='xFold' value='1.5' /> + <param name='tar' value='True' /> <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' /> </test> <test> <conditional name="tar_input_conditional"> - <param name="tar_input_selector" value='tar_input'/> - <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar"/> - <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar"/> - <param name="significantFiles" value="cHi-C/chicSignificantInteractions/significantFilesFolder.tar"/> + <param name="tar_input_selector" value='tar_input' /> + <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar" /> + <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar" /> + <param name="significantFiles" value="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" /> </conditional> <conditional name="batchmode_conditional"> - <param name="batchmode_selector" value='optionBatchmode'/> - <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> - <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/> - <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/> - <param name='computeSampleNumber' value='2'/> + <param name="batchmode_selector" value='optionBatchmode' /> + <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> + <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt' /> + <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt' /> + <param name='computeSampleNumber' value='2' /> </conditional> - <param name="pvalue" value='True'/> - <param name="truncateZeroPvalues" value='True'/> + <param name="pvalue" value='True' /> + <param name="truncateZeroPvalues" value='True' /> - <param name='backgroundModelFile' value='cHi-C/background.txt'/> - <param name='xFold' value='1.5'/> - <param name='tar' value='True'/> + <param name='backgroundModelFile' value='cHi-C/background.txt' /> + <param name='xFold' value='1.5' /> + <param name='tar' value='True' /> <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype='tar' compare="sim_size" delta='40000' /> </test> </tests> @@ -322,6 +307,6 @@ For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html -]]></help> +]]> </help> <expand macro="citations" /> </tool>