Mercurial > repos > bgruening > hicexplorer_hicaverageregions
diff hicAverageRegions.xml @ 8:c72fa6cb8817 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
| author | iuc |
|---|---|
| date | Wed, 18 Oct 2023 11:10:09 +0000 |
| parents | b15d27c440fd |
| children |
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--- a/hicAverageRegions.xml Tue Jan 10 19:09:18 2023 +0000 +++ b/hicAverageRegions.xml Wed Oct 18 11:10:09 2023 +0000 @@ -17,13 +17,14 @@ --rangeInBins '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange' #end if --coordinatesToBinMapping $coordinatesToBinMapping_selector + $considerStrandDirection --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." /> + <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"> @@ -44,6 +45,8 @@ <option value="center" selected="True">Center</option> <option value="end" selected="True">End</option> </param> + <param argument="--considerStrandDirection" type="boolean" truevalue="--considerStrandDirection" falsevalue="" label="Consider strand direction" help="This parameter specifies if the strand information is taken into account for the aggregation. It has the effect that the contacts of a reverse strand region are inverted e.g. [1,2,3] becomes [3,2,1]." /> + </inputs> <outputs> <data name="outFileName" from_work_dir="output_matrix.npz" format="zip" /> @@ -53,21 +56,21 @@ <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> <param name="regions" value="hicAverageRegions/regions.bed" ftype="bed"/> <conditional name="rangeFormat_conditional"> - <param name="rangeFormat_selector" value='optionGenomicUnits' /> - <param name="upstreamRange" value='100000' /> - <param name="downstreamRange" value='100000' /> + <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" /> + <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" ftype="bed" /> <conditional name="rangeFormat_conditional"> - <param name="rangeFormat_selector" value='optionBinUnits' /> - <param name="upstreamRange" value='100' /> - <param name="downstreamRange" value='100' /> + <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" /> + <output name="outFileName" file="hicAverageRegions/result_rangeInBins_100.npz" ftype="zip" compare="sim_size" delta="20000" /> </test> </tests> <help><![CDATA[