Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic
changeset 4:d6f5e51e97ec draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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--- a/chicAggregateStatistic.xml Tue Mar 24 13:47:20 2020 -0400 +++ b/chicAggregateStatistic.xml Fri Aug 14 06:19:12 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@WRAPPER_VERSION@.1"> <description>computes with a target file the to be tested regions for chicDifferentialTest</description> <macros> <token name="@BINARY@">chicAggregateStatistic</token> @@ -12,15 +12,27 @@ mkdir aggregatedFilesFolder && - #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 && + + #if $targetFiles: + ln -s '$tar_input_conditional.targetFiles' targetFiles.tar && + tar -C targetFolder -xvf targetFiles.tar && + #end if + #else: + #for $file in $tar_input_conditional.interactionFiles: + #set identifier = @ESCAPE_IDENTIFIER_FILE@ + ln -s '$file' 'interactionFiles/$identifier' && + #end for - #for $file in $targetFiles: - #set identifier = @ESCAPE_IDENTIFIER_FILE@ - ln -s '$file' 'targetFolder/$identifier' && - #end for + #for $file in $targetFiles: + #set identifier = @ESCAPE_IDENTIFIER_FILE@ + ln -s '$file' 'targetFolder/$identifier' && + #end for + + #end if + #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) @@ -44,10 +56,31 @@ -suffix aggregated.txt --threads @THREADS@ + #if $tar: + && cd aggregatedFilesFolder + && tar -cvf ../aggregatedFilesFolder.tar * + && cd .. + && rm -rf aggregatedFilesFolder + #end if + ]]></command> <inputs> - <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> - <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true"/> + + <conditional name="tar_input_conditional"> + <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> + <option value="tar_input">Tar file</option> + <option value="interval_input" selected="True">Interval files</option> + </param> + <when value="tar_input"> + <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/> + <param name='targetFiles' type="data" format="tar" label="Target files" multiple="false"/> + </when> + <when value="interval_input"> + <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> + <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true"/> + </when> + </conditional> + <conditional name="batchmode_conditional"> <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> @@ -62,14 +95,21 @@ <when value="optionSinglemode"> </when> </conditional> + <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file" + help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/> + </inputs> <outputs> <collection name="aggregatedFilesCollection" type="list" label="Aggregated files"> + <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" /> </collection> <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${tool.name} aggregated file names"> <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> </data> + <data name="aggregatedFilesFolderTar" from_work_dir="aggregatedFilesFolder.tar" format="tar" label="Aggregated files tar.gz"> + <filter>tar</filter> + </data> </outputs> <tests> <test> @@ -108,6 +148,44 @@ <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.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/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_19093103_19093103_Tfap2d.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_4487435_4487435_Sox17.txt"/> + <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.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="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/> + </conditional> + + <param name='tar' value='True'/> + + <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' /> + <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.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/chicViewpoint/output_1.tar"/> + <param name="targetFiles" value="cHi-C/chicSignificantInteractions/targetFolder.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="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/> + </conditional> + + <param name='tar' value='True'/> + + <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' /> + <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/> + </test> </tests> <help><![CDATA[
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