Mercurial > repos > bgruening > hicexplorer_chicdifferentialtest
changeset 4:126abc4b03f1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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--- a/chicDifferentialTest.xml Tue Mar 24 14:03:15 2020 -0400 +++ b/chicDifferentialTest.xml Fri Aug 14 06:15:21 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@WRAPPER_VERSION@.1"> <description>computes differential interactions of viewpoints</description> <macros> <token name="@BINARY@">chicDifferentialTest</token> @@ -11,11 +11,16 @@ mkdir interactionFiles && mkdir differentialFolder && - #for $file in $interactionFiles: - #set identifier = @ESCAPE_IDENTIFIER_FILE@ - ln -s '$file' 'interactionFiles/$identifier' && - #end for - + #if $tar_input_conditional.tar_input_selector == 'tar_input': + ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && + tar -C interactionFiles -xvf viewpoints.tar && + #else: + #for $file in $tar_input_conditional.interactionFiles: + #set identifier = @ESCAPE_IDENTIFIER_FILE@ + + ln -s '$file' 'interactionFiles/$identifier' && + #end for + #end if #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) #end if @@ -32,9 +37,27 @@ --alpha $alpha --outputFolder differentialFolder --threads @THREADS@ + + #if $tar: + && cd differentialFolder + && tar -cvf ../differentialFolder.tar * + && cd .. + && rm -rf differentialFolder + #end if ]]></command> <inputs> + <conditional name="tar_input_conditional"> + <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> + <option value="tar_input">tar file</option> + <option value="interval_input" selected="True">Interval files</option> + </param> + <when value="tar_input"> + <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/> + </when> + <when value="interval_input"> <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> + </when> + </conditional> <conditional name="batchmode_conditional"> <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> @@ -52,6 +75,9 @@ <option value="fisher" selected="True">Fisher exact</option> <option value="chi2">Chi2 contingency</option> </param> + <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file" + help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/> + </inputs> <outputs> <collection name="differentialFolderCollection" type="list" label="Differential test files"> @@ -60,10 +86,16 @@ <data name="rejectedFileNames" from_work_dir="rejected_H0.txt" format="txt" label="${tool.name} rejected H0"> <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> </data> + <data name="differentialFolderTar" from_work_dir="differentialFolder.tar" format="tar" label="Differential test files tar.gz"> + <filter>tar</filter> + </data> </outputs> <tests> <test> - <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"/> + <conditional name="tar_input_conditional"> + <param name="tar_input_selector" value='interval_input'/> + <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"/> + </conditional> <conditional name="batchmode_conditional"> <param name="batchmode_selector" value='optionBatchmode'/> @@ -90,7 +122,11 @@ <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000'/> </test> <test> - <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"/> + <conditional name="tar_input_conditional"> + <param name="tar_input_selector" value='interval_input'/> + <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"/> + + </conditional> <conditional name="batchmode_conditional"> <param name="batchmode_selector" value='optionSinglemode'/> @@ -104,6 +140,45 @@ <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"/> </output_collection> </test> + + + <test> + <conditional name="tar_input_conditional"> + <param name="tar_input_selector" value='interval_input'/> + <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"/> + </conditional> + + <conditional name="batchmode_conditional"> + <param name="batchmode_selector" value='optionBatchmode'/> + <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/> + </conditional> + <param name="statisticTest_selector" value='chi2'/> + <param name="alpha" value='0.5'/> + <param name='tar' value='True'/> + + <output name="differentialFolderTar" file="cHi-C/chicDifferentialTest/batch_mode_chi2.tar" ftype='tar' compare="sim_size" delta='40000' /> + + <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" 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/chicAggregateStatistic/batch_mode.tar"/> + </conditional> + + <conditional name="batchmode_conditional"> + <param name="batchmode_selector" value='optionBatchmode'/> + <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/> + </conditional> + <param name="statisticTest_selector" value='chi2'/> + <param name="alpha" value='0.5'/> + <param name='tar' value='True'/> + + <output name="differentialFolderTar" file="cHi-C/chicDifferentialTest/batch_mode_chi2.tar" ftype='tar' compare="sim_size" delta='40000' /> + + <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000'/> + </test> </tests> <help><![CDATA[
Binary file test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png has changed
Binary file test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png has changed
Binary file test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png has changed