Mercurial > repos > bgruening > hicexplorer_chicdifferentialtest
diff chicDifferentialTest.xml @ 2:1e52af48d34e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author | iuc |
---|---|
date | Wed, 11 Mar 2020 17:10:43 -0400 |
parents | fa6fc09ba259 |
children | 126abc4b03f1 |
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--- a/chicDifferentialTest.xml Wed Feb 05 19:42:44 2020 -0500 +++ b/chicDifferentialTest.xml Wed Mar 11 17:10:43 2020 -0400 @@ -44,14 +44,14 @@ <when value="optionBatchmode"> <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/> </when> - <when value="optionSinglemode"> + <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='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> </inputs> <outputs> <collection name="differentialFolderCollection" type="list" label="Differential test files"> @@ -63,8 +63,8 @@ </outputs> <tests> <test> - <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed"/> - + <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="batchmode_conditional"> <param name="batchmode_selector" value='optionBatchmode'/> <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/> @@ -72,26 +72,26 @@ <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.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed" ftype="interval" lines_diff="4"/> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed" ftype="interval" lines_diff="4"/> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed" ftype="interval" lines_diff="4"/> + <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.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed" ftype="interval" lines_diff="4"/> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed" ftype="interval" lines_diff="4"/> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed" ftype="interval" lines_diff="4"/> - - <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed" ftype="interval" lines_diff="4"/> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed" ftype="interval" lines_diff="4"/> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed" 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> - <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed"/> - + <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="batchmode_conditional"> <param name="batchmode_selector" value='optionSinglemode'/> </conditional> @@ -99,9 +99,9 @@ <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.bed" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed" ftype="interval" lines_diff="4"/> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed" ftype="interval" lines_diff="4"/> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed" ftype="interval" lines_diff="4"/> + <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> </tests> @@ -110,8 +110,8 @@ Differential testing of two viewpoints ====================================== -chicDifferentialTest tests if two locations under consideration of the reference point have a different interaction count. For this either Fisher's test or chi2 contingency test can be used. -The files that are accepted 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. +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_