Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic
diff chicAggregateStatistic.xml @ 7:554e8a6cec27 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
| author | iuc |
|---|---|
| date | Mon, 01 Jul 2024 18:52:21 +0000 |
| parents | ed8e77d5d654 |
| children |
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--- a/chicAggregateStatistic.xml Tue Jan 10 18:19:18 2023 +0000 +++ b/chicAggregateStatistic.xml Mon Jul 01 18:52:21 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> +<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>computes with a target file the to be tested regions for chicDifferentialTest</description> <macros> <token name="@BINARY@">chicAggregateStatistic</token> @@ -7,170 +7,63 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ #import re - mkdir interactionFiles && - mkdir targetFolder && - mkdir aggregatedFilesFolder && - - #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 && + + @BINARY@ + + --interactionFile '$interactionFile' + --outFileName aggregatedFile.hdf5 + #if $targetFormat_conditional.targetFormat_selector == 'hdf5': + --targetFile '$targetFormat_conditional.targetFileHDF' + #else: + --targetFile '$targetFormat_conditional.targetFileBED' #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 - #end if - - #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': - #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) - #set $targetfileslist = ' '.join([ 'targetFolder/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $targetFiles ]) - #end if - @BINARY@ - #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': - --interactionFile $interactonfileslist - --targetFile $targetfileslist - #else: - --interactionFile $batchmode_conditional.interactionFilesOrderFile - --interactionFileFolder interactionFiles - --targetFileFolder targetFolder - --targetFile $batchmode_conditional.targetFilesOrderFile - --batchMode - --writeFileNamesToFile aggregatedFilesBatch.txt - #end if - - --outputFolder aggregatedFilesFolder - -suffix aggregated.txt --threads @THREADS@ - #if $tar: - && cd aggregatedFilesFolder - && tar -cvf ../aggregatedFilesFolder.tar * - && cd .. - && rm -rf aggregatedFilesFolder - #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 name="interactionFile" type="data" format="h5" label="The interaction data file created by chicViewpoint" /> + <conditional name="targetFormat_conditional"> + <param name="targetFormat_selector" type="select" label="List of chromosomes or a BED file containg regions"> + <option value="hdf5">Target file from chicSignificantInteractions (h5 / hdf5)</option> + <option value="bed" selected="True">Regions of interest (bed)</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 value="hdf5"> + <param name="targetFileHDF" type="data" format="h5" label="The target data file created by chicSignificantInteractions" /> </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 value="bed"> + <param name="targetFileBED" type="data" format="bed" label="Regions of interest" help="BED file which stores a list of regions that are used to aggregate the data for the differntial test." /> </when> </conditional> - - <conditional name="batchmode_conditional"> - <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> - <option value="optionBatchmode">Batch processing</option> - <option value="optionSinglemode" selected="True">Single file processing</option> - </param> - <when value="optionBatchmode"> - <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" /> - <param name='targetFilesOrderFile' type="data" format="txt" label="Target file order" /> - </when> - <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> + </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> + <data name="aggregatedFile" from_work_dir="aggregatedFile.hdf5" format="h5" label="Aggregated file" /> </outputs> <tests> <test> - <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 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' /> + <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" /> + <conditional name="targetFormat_conditional"> + <param name="targetFormat_selector" value="hdf5" /> + <param name="targetFileHDF" value="cHi-C/chicSignificantInteractions/targetFile_dual.hdf5" /> </conditional> - - <output_collection name="aggregatedFilesCollection" type="list" count="6"> - <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4" /> - <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4" /> - <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4" /> - <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4" /> - <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4" /> - <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4" /> - </output_collection> - <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" /> + <output name="aggregatedFile" ftype="h5"> + <assert_contents> + <has_h5_attribute key="type" value="aggregate" /> + </assert_contents> + </output> </test> <test> - <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" /> - <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" /> - - <conditional name="batchmode_conditional"> - <param name="batchmode_selector" value='optionSinglemode' /> - </conditional> - - <output_collection name="aggregatedFilesCollection" type="list" count="2"> - <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4" /> - <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> + <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" /> - <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 name="targetFormat_conditional"> + <param name="targetFormat_selector" value="bed" /> + <param name="targetFileBED" value="cHi-C/target_list.bed" /> </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" /> - </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" /> + <output name="aggregatedFile" ftype="h5"> + <assert_contents> + <has_h5_attribute key="type" value="aggregate" /> + </assert_contents> + </output> </test> </tests> <help><![CDATA[