Mercurial > repos > bgruening > hicexplorer_chicdifferentialtest
view chicDifferentialTest.xml @ 9:57aeaf6b237d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author | iuc |
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date | Mon, 01 Jul 2024 19:50:00 +0000 |
parents | 9d42a6133690 |
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<tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <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 @BINARY@ --aggregatedFile $aggregatedFile --statisticTest $statisticTest_selector --alpha $alpha --outFileName differentialFile.hdf5 --threads @THREADS@ ]]> </command> <inputs> <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> </inputs> <outputs> <data name="differentialFile" from_work_dir="differentialFile.hdf5" format="h5" label="Differential test file" /> </outputs> <tests> <test> <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[ 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>