| Previous changeset 3:dbf82dd7bdb3 (2020-03-24) Next changeset 5:46793007f090 (2020-12-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e" |
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modified:
chicPlotViewpoint.xml test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png test-data/cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png |
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added:
test-data/cHi-C/chicAggregateStatistic/batch_mode.tar test-data/cHi-C/chicDifferentialTest/batch_mode_chi2.tar test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar test-data/cHi-C/chicPlotViewpoint/batchMode/plots.tar test-data/cHi-C/chicSignificantInteractions/significantFilesFolder.tar test-data/cHi-C/chicSignificantInteractions/targetFolder.tar test-data/cHi-C/chicViewpoint/output_1.tar test-data/cHi-C/chicViewpoint/viewpoints.tar |
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| diff -r dbf82dd7bdb3 -r ac7999229ac6 chicPlotViewpoint.xml --- a/chicPlotViewpoint.xml Tue Mar 24 14:12:09 2020 -0400 +++ b/chicPlotViewpoint.xml Fri Aug 14 06:02:35 2020 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">\n+<tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1">\n <description>creates plots for viewpoints</description>\n <macros>\n <token name="@BINARY@">chicPlotViewpoint</token>\n@@ -13,41 +13,51 @@\n mkdir significantFolder &&\n mkdir plots &&\n \n+ #if $tar_input_conditional.tar_input_selector == \'tar_input\':\n+ ln -s \'$tar_input_conditional.interactionFiles\' viewpoints.tar && \n+ tar -C interactionFiles -xvf viewpoints.tar &&\n \n- #for $file in $interactionFiles:\n- #set identifier = @ESCAPE_IDENTIFIER_FILE@\n- ln -s \'$file\' \'interactionFiles/$identifier\' &&\n- #end for\n+ #if $differentialFiles:\n+ ln -s \'$tar_input_conditional.differentialFiles\' differential.tar && \n+ tar -C differentialFolder -xvf differential.tar &&\n+ #end if\n+ #if $significantFiles:\n+ ln -s \'$tar_input_conditional.significantFiles\' significantFiles.tar && \n+ tar -C significantFolder -xvf significantFiles.tar &&\n+ #end if\n+ #else:\n+ #for $file in $tar_input_conditional.interactionFiles:\n+ #set identifier = @ESCAPE_IDENTIFIER_FILE@\n+ ln -s \'$file\' \'interactionFiles/$identifier\' &&\n+ #end for\n \n- #if $differentialFiles:\n- #for $file in $differentialFiles:\n- #set identifier = @ESCAPE_IDENTIFIER_FILE@\n- ln -s \'$file\' \'differentialFolder/$identifier\' &&\n+ #for $file in $tar_input_conditional.differentialFiles:\n+ #set identifier = @ESCAPE_IDENTIFIER_FILE@\n+ ln -s \'$file\' \'differentialFolder/$identifier\' &&\n+ #end for\n+\n+ #for $file in $tar_input_conditional.significantFiles:\n+ #set identifier = @ESCAPE_IDENTIFIER_FILE@\n+ ln -s \'$file\' \'significantFolder/$identifier\' &&\n #end for\n #end if\n \n- #if $significantFiles:\n- #for $file in $significantFiles:\n- #set identifier = @ESCAPE_IDENTIFIER_FILE@\n- ln -s \'$file\' \'significantFolder/$identifier\' &&\n- #end for\n- #end if\n \n #if $batchmode_conditional.batchmode_selector == \'optionSinglemode\':\n- #set $interactonfileslist = \' \'.join([ \'\\\'interactionFiles/%s\\\'\' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])\n- #set $differentialfileslist = \' \'.join([ \'\\\'differentialFolder/%s\\\'\' % @ESCAPE_IDENTIFIER_FILE@ for $file in $differentialFiles ])\n- #set $significantfileslist = \' \'.join([ \'\\\'significantFolder/%s\\\'\' % @ESCAPE_IDENTIFIER_FILE@ for $file in $significantFiles ])\n+ #set $interactonfileslist = \' \'.join([ \'\\\'interactionFiles/%s\\\'\' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.interactionFiles ])\n+ #set $differentialfileslist = \' \'.join([ \'\\\'differentialFolder/%s\\\'\' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.differentialFiles ])\n+ #set $significantfileslist = \' \'.join([ \'\\\'significantFolder/%s\\\'\' % @ESCAPE_IDENTIFIER_FILE@ for $file in $tar_input_conditional.significantFiles ])\n \n #end if\n \n @BINARY@\n #if $batchmode_conditional.batchmode_selector == \'optionSinglemode\':\n --interactionFile $interactonfileslist\n- #if $differentialFiles:\n+ #if $tar_input_conditional.differentialFiles:\n --differentialTestResult $differentialfileslist\n #end if\n \n- #if $significantFiles:\n+ #if $tar_input_conditional.significantFiles:\n --significantInteractions $significantfileslist\n #end if\n \n@@ -104,14 +114,34 @@\n #if $batchm'..b'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"/>\n+ <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"/>\n+ </conditional>\n \n <conditional name="batchmode_conditional">\n- <param name="batchmode_selector" value=\'optionSinglemode\'/>\n+ <param name="batchmode_selector" value=\'optionBatchmode\'/>\n+ <param name="interactionFilesOrderFile" value=\'cHi-C/chicViewpoint/fileNames_two_matrices.txt\'/>\n+ <param name="differentialFilesOrderFile" value=\'cHi-C/chicDifferentialTest/rejectedFilesList.txt\'/>\n+ <param name="significantInteractionFilesOrderFile" value=\'cHi-C/chicSignificantInteractions/output_5_significant_files.txt\'/>\n+ <param name=\'computeSampleNumber\' value=\'2\'/>\n+ </conditional>\n+ <param name="pvalue" value=\'True\'/>\n+ <param name="truncateZeroPvalues" value=\'True\'/>\n+\n+ <param name=\'backgroundModelFile\' value=\'cHi-C/background.txt\'/>\n+ <param name=\'xFold\' value=\'1.5\'/>\n+ <param name=\'tar\' value=\'True\'/>\n+ <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype=\'tar\' compare="sim_size" delta=\'40000\' />\n+ </test>\n+\n+ <test>\n+ <conditional name="tar_input_conditional">\n+ <param name="tar_input_selector" value=\'tar_input\'/>\n+ <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar"/>\n+ <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar"/>\n+ <param name="significantFiles" value="cHi-C/chicSignificantInteractions/significantFilesFolder.tar"/>\n </conditional>\n \n- <output_collection name="plotsCollection" type="list" count="1">\n- <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare=\'sim_size\' delta=\'40000\'/>\n+ <conditional name="batchmode_conditional">\n+ <param name="batchmode_selector" value=\'optionBatchmode\'/>\n+ <param name="interactionFilesOrderFile" value=\'cHi-C/chicViewpoint/fileNames_two_matrices.txt\'/>\n+ <param name="differentialFilesOrderFile" value=\'cHi-C/chicDifferentialTest/rejectedFilesList.txt\'/>\n+ <param name="significantInteractionFilesOrderFile" value=\'cHi-C/chicSignificantInteractions/output_5_significant_files.txt\'/>\n+ <param name=\'computeSampleNumber\' value=\'2\'/>\n+ </conditional>\n+ <param name="pvalue" value=\'True\'/>\n+ <param name="truncateZeroPvalues" value=\'True\'/>\n \n- </output_collection>\n+ <param name=\'backgroundModelFile\' value=\'cHi-C/background.txt\'/>\n+ <param name=\'xFold\' value=\'1.5\'/>\n+ <param name=\'tar\' value=\'True\'/>\n+ <output name="plotsTar" file="cHi-C/chicPlotViewpoint/batchMode/plots.tar" ftype=\'tar\' compare="sim_size" delta=\'40000\' />\n </test>\n </tests>\n <help><
