| Previous changeset 3:7668fac6cc3a (2020-03-24) Next changeset 5:6bc82c6d6620 (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:
chicSignificantInteractions.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 7668fac6cc3a -r 38fa8a72ece6 chicSignificantInteractions.xml --- a/chicSignificantInteractions.xml Tue Mar 24 13:42:40 2020 -0400 +++ b/chicSignificantInteractions.xml Fri Aug 14 05:59:38 2020 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.0">\n+<tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.1">\n <description>computes viewpoints with the given reference points and a background model</description>\n <macros>\n <token name="@BINARY@">chicSignificantInteractions</token>\n@@ -12,12 +12,17 @@\n mkdir targetFolder &&\n mkdir significantFilesFolder &&\n \n- #for $file in $interactionFiles:\n- #set identifier = @ESCAPE_IDENTIFIER_FILE@\n-\n- ln -s \'$file\' \'interactionFiles/$identifier\' &&\n- #end for\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+ #else:\n+ #for $file in $tar_input_conditional.interactionFiles:\n+ #set identifier = @ESCAPE_IDENTIFIER_FILE@\n+ \n+ ln -s \'$file\' \'interactionFiles/$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 #end if\n@@ -53,9 +58,36 @@\n --fixateRange $fixateRange\n -suffix significant_interactions.txt\n --threads @THREADS@\n+\n+ #if $tar:\n+ && cd targetFolder\n+ && tar -cvf ../targetFolder.tar *\n+ && cd ..\n+ && rm -rf targetFolder\n+\n+ && cd significantFilesFolder\n+ && tar -cvf ../significantFilesFolder.tar *\n+ && cd ..\n+ && rm -rf significantFilesFolder\n+\n+ #end if\n ]]></command>\n <inputs>\n+ <conditional name="tar_input_conditional">\n+ <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">\n+ <option value="tar_input">Tar file</option>\n+ <option value="interval_input" selected="True">Interval files</option>\n+ </param>\n+ <when value="tar_input">\n+ <param name=\'interactionFiles\' type="data" format="tar" label="Interaction files" multiple="false"/>\n+ </when>\n+ <when value="interval_input">\n <param name=\'interactionFiles\' type="data" format="interval" label="Interaction files" multiple="true"/>\n+ </when>\n+ </conditional>\n+\n+\n+\n <conditional name="batchmode_conditional">\n <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">\n <option value="optionBatchmode">Batch processing</option>\n@@ -96,6 +128,8 @@\n <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help=\'Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.\'/>\n <param name=\'truncateZeroPvalues\' type=\'boolean\' truevalue=\'--truncateZeroPvalues\' falsevalue="" checked="false" label="Truncate zeros by setting them to one."\n help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision."/>\n+ <param name=\'tar\' type=\'boolean\' checked="false" truevalue=\'True\' label="tar output to one file"\n+ help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>\n </inputs>\n <outputs>\n <collection name="significantFilesCollection" type="list" label="Significant files">\n@@ -110,10 +144,19 @@\n <data name="targetFileNames" from_work_dir="targetListFile.txt'..b'test> \n+\n+ <test>\n+ <conditional name="tar_input_conditional">\n+ <param name="tar_input_selector" value=\'interval_input\'/>\n+ <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>\n+ </conditional>\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="computeSampleNumber" value=\'2\'/>\n+ </conditional>\n+ <param name="pvalue" value=\'0.2\'/>\n+\n+ <conditional name="filter_conditional">\n+ <param name="filter_selector" value=\'optionLoosePvalue\'/>\n+ <param name="loosePvalue" value=\'0.5\'/>\n+ </conditional>\n+\n+ <param name="backgroundModelFile" value="cHi-C/background.txt"/>\n+ <param name="rangeUpstream" value="200000"/>\n+ <param name="rangeDownstream" value="200000"/>\n+\n+ <param name=\'tar\' value=\'True\'/>\n+\n+ <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype=\'tar\' compare="sim_size" delta=\'40000\' />\n+ <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype=\'tar\' compare="sim_size" delta=\'40000\' />\n+\n+ <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta=\'40000\'/>\n+ <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" 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/viewpoints.tar"/>\n+ </conditional>\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="computeSampleNumber" value=\'2\'/>\n+ </conditional>\n+ <param name="pvalue" value=\'0.2\'/>\n+\n+ <conditional name="filter_conditional">\n+ <param name="filter_selector" value=\'optionLoosePvalue\'/>\n+ <param name="loosePvalue" value=\'0.5\'/>\n+ </conditional>\n+\n+ <param name="backgroundModelFile" value="cHi-C/background.txt"/>\n+ <param name="rangeUpstream" value="200000"/>\n+ <param name="rangeDownstream" value="200000"/>\n+\n+ <param name=\'tar\' value=\'True\'/>\n+\n+ <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype=\'tar\' compare="sim_size" delta=\'40000\' />\n+ <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype=\'tar\' compare="sim_size" delta=\'40000\' />\n+\n+ <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta=\'40000\'/>\n+ <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta=\'40000\'/>\n </test>\n \n </tests>\n' |
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