| Previous changeset 3:9180983da5c2 (2020-03-24) Next changeset 5:8c5cecbfc3aa (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:
chicDifferentialTest.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 9180983da5c2 -r 126abc4b03f1 chicDifferentialTest.xml --- a/chicDifferentialTest.xml Tue Mar 24 14:03:15 2020 -0400 +++ b/chicDifferentialTest.xml Fri Aug 14 06:15:21 2020 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@WRAPPER_VERSION@.0">\n+<tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@WRAPPER_VERSION@.1">\n <description>computes differential interactions of viewpoints</description>\n <macros>\n <token name="@BINARY@">chicDifferentialTest</token>\n@@ -11,11 +11,16 @@\n mkdir interactionFiles &&\n mkdir differentialFolder &&\n \n- #for $file in $interactionFiles:\n- #set identifier = @ESCAPE_IDENTIFIER_FILE@\n- ln -s \'$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 #if $batchmode_conditional.batchmode_selector == \'optionSinglemode\':\n #set $interactonfileslist = \' \'.join([ \'\\\'interactionFiles/%s\\\'\' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])\n #end if\n@@ -32,9 +37,27 @@\n --alpha $alpha\n --outputFolder differentialFolder\n --threads @THREADS@\n+\n+ #if $tar:\n+ && cd differentialFolder\n+ && tar -cvf ../differentialFolder.tar *\n+ && cd ..\n+ && rm -rf differentialFolder\n+ #end if\n ]]></command>\n <inputs>\n+ <conditional name="tar_input_conditional">\n+ <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">\n+ <option value="tar_input">tar file</option>\n+ <option value="interval_input" selected="True">Interval files</option>\n+ </param>\n+ <when value="tar_input">\n+ <param name=\'interactionFiles\' type="data" format="tar" label="Interaction files" multiple="false"/>\n+ </when>\n+ <when value="interval_input">\n <param name=\'interactionFiles\' type="data" format="interval" label="Interaction files" multiple="true"/>\n+ </when>\n+ </conditional>\n \n <conditional name="batchmode_conditional">\n <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">\n@@ -52,6 +75,9 @@\n <option value="fisher" selected="True">Fisher exact</option>\n <option value="chi2">Chi2 contingency</option>\n </param>\n+ <param name=\'tar\' type=\'boolean\' checked="false" truevalue=\'True\' label="tar output to one file"\n+ help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>\n+ \n </inputs>\n <outputs>\n <collection name="differentialFolderCollection" type="list" label="Differential test files">\n@@ -60,10 +86,16 @@\n <data name="rejectedFileNames" from_work_dir="rejected_H0.txt" format="txt" label="${tool.name} rejected H0">\n <filter>batchmode_conditional.batchmode_selector == \'optionBatchmode\'</filter>\n </data>\n+ <data name="differentialFolderTar" from_work_dir="differentialFolder.tar" format="tar" label="Differential test files tar.gz">\n+ <filter>tar</filter>\n+ </data>\n </outputs>\n <tests>\n <test>\n- <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt,cHi-'..b'e=\'optionBatchmode\'/>\n@@ -90,7 +122,11 @@\n <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta=\'40000\'/>\n </test>\n <test>\n- <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt"/>\n+ <conditional name="tar_input_conditional">\n+ <param name="tar_input_selector" value=\'interval_input\'/>\n+ <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt"/>\n+\n+ </conditional>\n \n <conditional name="batchmode_conditional">\n <param name="batchmode_selector" value=\'optionSinglemode\'/>\n@@ -104,6 +140,45 @@\n <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt" ftype="interval" lines_diff="4"/>\n </output_collection>\n </test>\n+\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/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt"/>\n+ </conditional>\n+\n+ <conditional name="batchmode_conditional">\n+ <param name="batchmode_selector" value=\'optionBatchmode\'/>\n+ <param name="interactionFilesOrderFile" value=\'cHi-C/chicAggregateStatistic/batch_mode_file_names.txt\'/>\n+ </conditional>\n+ <param name="statisticTest_selector" value=\'chi2\'/>\n+ <param name="alpha" value=\'0.5\'/>\n+ <param name=\'tar\' value=\'True\'/>\n+\n+ <output name="differentialFolderTar" file="cHi-C/chicDifferentialTest/batch_mode_chi2.tar" ftype=\'tar\' compare="sim_size" delta=\'40000\' />\n+\n+ <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.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/chicAggregateStatistic/batch_mode.tar"/>\n+ </conditional>\n+\n+ <conditional name="batchmode_conditional">\n+ <param name="batchmode_selector" value=\'optionBatchmode\'/>\n+ <param name="interactionFilesOrderFile" value=\'cHi-C/chicAggregateStatistic/batch_mode_file_names.txt\'/>\n+ </conditional>\n+ <param name="statisticTest_selector" value=\'chi2\'/>\n+ <param name="alpha" value=\'0.5\'/>\n+ <param name=\'tar\' value=\'True\'/>\n+\n+ <output name="differentialFolderTar" file="cHi-C/chicDifferentialTest/batch_mode_chi2.tar" ftype=\'tar\' compare="sim_size" delta=\'40000\' />\n+\n+ <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta=\'40000\'/>\n+ </test>\n </tests>\n <help><
