Mercurial > repos > bgruening > hicexplorer_hicaverageregions
view hicAverageRegions.xml @ 5:2818b428a5c5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3e5c2f8ce3e540b0474746a33ee20b4a374dd38c"
author | iuc |
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date | Fri, 11 Dec 2020 20:57:08 +0000 |
parents | 4b6a36c18e5e |
children | 03d7978293fe |
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<tool id="hicexplorer_hicaverageregions" name="@BINARY@" version="@WRAPPER_VERSION@.0"> <description>sums Hi-C contacts around given reference points and computes their average.</description> <macros> <token name="@BINARY@">hicAverageRegions</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' && @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext' --regions '$regions' #if $rangeFormat_conditional.rangeFormat_selector == 'optionGenomicUnits': --range '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange' #else: --rangeInBins '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange' #end if --coordinatesToBinMapping $coordinatesToBinMapping_selector --outFileName output_matrix.npz ]]> </command> <inputs> <expand macro='matrix_h5_cooler_macro' /> <param argument="--regions" type="data" format='bed' label="Regions to average" help="BED file which stores a list of regions that are summed and averaged."/> <conditional name="rangeFormat_conditional"> <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions"> <option value="optionGenomicUnits">Range in genomic units</option> <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option> </param> <when value="optionGenomicUnits"> <param name="upstreamRange" type="integer" value="" label="Upstream range"/> <param name="downstreamRange" type="integer" value="" label="Downstream range"/> </when> <when value="optionBinUnits"> <param name="upstreamRange" type="integer" value="" label="Upstream range"/> <param name="downstreamRange" type="integer" value="" label="Downstream range"/> </when> </conditional> <param name="coordinatesToBinMapping_selector" type="select" label="Define start value of range" help="If the region contains start and end coordinates, define if the start, center (start + (end-start) / 2) or end bin should be used as start for range."> <option value="start">Start</option> <option value="center" selected="True">Center</option> <option value="end" selected="True">End</option> </param> </inputs> <outputs> <data name="outFileName" from_work_dir="output_matrix.npz" format="zip"/> </outputs> <tests> <test> <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> <param name="regions" value="hicAverageRegions/regions.bed" /> <conditional name="rangeFormat_conditional"> <param name="rangeFormat_selector" value='optionGenomicUnits'/> <param name="upstreamRange" value='100000'/> <param name="downstreamRange" value='100000'/> </conditional> <output name='outFileName' file='hicAverageRegions/result_range_100000.npz' ftype="zip" compare="sim_size" delta="20000" /> </test> <test> <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> <param name="regions" value="hicAverageRegions/regions.bed" /> <conditional name="rangeFormat_conditional"> <param name="rangeFormat_selector" value='optionBinUnits'/> <param name="upstreamRange" value='100'/> <param name="downstreamRange" value='100'/> </conditional> <output name='outFileName' file='hicAverageRegions/result_rangeInBins_100.npz' ftype="zip" compare="sim_size" delta="20000" /> </test> </tests> <help><![CDATA[ Average regions =============== This tool sums Hi-C contacts around given reference points and computes their average. This tool is useful to detect differences at certain reference points, TAD boundaries for instance, between samples. WARNING: This tool can only be used with fixed bin size Hi-C matrices. No guarantees how and if it works on restriction site interaction matrices. Use the output to plot the average with hicPlotAverageRegions. _________________ | 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>