Mercurial > repos > bgruening > hicexplorer_chicdifferentialtest
diff chicDifferentialTest.xml @ 8:9d42a6133690 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
| author | iuc |
|---|---|
| date | Wed, 18 Oct 2023 10:23:20 +0000 |
| parents | 975b6a67e4b0 |
| children | 57aeaf6b237d |
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--- a/chicDifferentialTest.xml Tue Jan 10 18:51:28 2023 +0000 +++ b/chicDifferentialTest.xml Wed Oct 18 10:23:20 2023 +0000 @@ -7,162 +7,35 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ #import re - - mkdir interactionFiles && - mkdir differentialFolder && - - #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 @BINARY@ - #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': - --interactionFile $interactonfileslist - #else: - --interactionFile $batchmode_conditional.interactionFilesOrderFile - --interactionFileFolder interactionFiles - --batchMode - --rejectedFileNamesToFile rejected_H0.txt - #end if + --aggregatedFile $aggregatedFile --statisticTest $statisticTest_selector --alpha $alpha - --outputFolder differentialFolder + --outFileName differentialFile.hdf5 --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"> - <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" /> - </when> - <when value="optionSinglemode"> - </when> - </conditional> - <param name='alpha' type="float" value='2.0' label="Alpha" help='Accept all samples to significance level alpha.' /> + <param name="aggregatedFile" type="data" format="h5" label="The aggregated data file created by chicAggregateStatistic" /> + <param name="alpha" type="float" value="2.0" label="Alpha" help="Accept all samples to significance level alpha." /> <param name="statisticTest_selector" type="select" label="Statistical test"> <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"> - <discover_datasets pattern="__name__" format="interval" directory="differentialFolder" /> - </collection> - <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> + <data name="differentialFile" from_work_dir="differentialFile.hdf5" format="h5" label="Differential test file" /> </outputs> <tests> <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' /> - <output_collection name="differentialFolderCollection" type="list" count="9"> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt" ftype="interval" lines_diff="4" /> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt" ftype="interval" lines_diff="4" /> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt" ftype="interval" lines_diff="4" /> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt" ftype="interval" lines_diff="4" /> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt" ftype="interval" lines_diff="4" /> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt" ftype="interval" lines_diff="4" /> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt" ftype="interval" lines_diff="4" /> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt" ftype="interval" lines_diff="4" /> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt" ftype="interval" lines_diff="4" /> - </output_collection> - - <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='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' /> - </conditional> - <param name="statisticTest_selector" value='fisher' /> - <param name="alpha" value='0.5' /> - <output_collection name="differentialFolderCollection" type="list" count="3"> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt" ftype="interval" lines_diff="4" /> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt" ftype="interval" lines_diff="4" /> - <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" /> - </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" /> + <param name="aggregatedFile" value="cHi-C/chicAggregateStatistic/aggregate.hdf5" /> + <param name="statisticTest_selector" value="chi2" /> + <param name="alpha" value="0.5" /> + <output name="differentialFile" ftype="h5"> + <assert_contents> + <has_h5_attribute key="type" value="differential" /> + </assert_contents> + </output> </test> </tests> <help><![CDATA[