Mercurial > repos > bgruening > hicexplorer_chicdifferentialtest
view chicDifferentialTest.xml @ 6:975b6a67e4b0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author | iuc |
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date | Tue, 16 Mar 2021 15:16:02 +0000 |
parents | 126abc4b03f1 |
children | 9d42a6133690 |
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<tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>computes differential interactions of viewpoints</description> <macros> <token name="@BINARY@">chicDifferentialTest</token> <import>macros.xml</import> </macros> <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 --statisticTest $statisticTest_selector --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"> <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="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> </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" /> </test> </tests> <help><![CDATA[ Differential testing of two viewpoints ====================================== chicDifferentialTest tests if two locations under consideration of the reference point have a different interaction count. Either Fisher's test or chi2 contingency test can be used. Input files for this test can be created with `chicAggregateStatistic`. H0 is assuming the interactions are not different. Therefore the differential interaction counts are all where H0 was rejected. For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html ]]> </help> <expand macro="citations" /> </tool>