Mercurial > repos > bgruening > hicexplorer_hicadjustmatrix
view hicAdjustMatrix.xml @ 11:e8760fc0e29b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
author | iuc |
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date | Thu, 05 Dec 2024 18:39:17 +0000 |
parents | 2dccb6bb0add |
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<tool id="hicexplorer_hicadjustmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>adjust the shape of a Hi-C matrix</description> <macros> <token name="@BINARY@">hicAdjustMatrix</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ #set matrix_name = 'matrix_in.' + str($matrix_h5_cooler.ext) #set matrix_file_out = 'matrix_out.' + str($matrix_h5_cooler.ext) ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' && @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext' --action $action_selector --outFileName '$matrix_file_out' #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionChromosomes": ## special: --chromosomeOrder is optional, but if given it needs at least one argument #set chroms = '\' \''.join([ str($var.chromosome) for $var in $chromosomeOrRegionFile_conditional.chromosomeOrder ]) #if chroms: --chromosomes '$chroms' #end if #end if #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionRegionFile": --regions '$chromosomeOrRegionFile_conditional.regions' #end if #if not $interIntra_selector == 'keep': --interIntraHandling $interIntra_selector #end if && mv '$matrix_file_out' matrix ]]> </command> <inputs> <expand macro="matrix_h5_cooler_macro" /> <param name="action_selector" type="select" label="Apply action"> <option value="keep" selected="True">keep</option> <option value="remove">remove</option> <option value="mask">mask</option> </param> <conditional name="chromosomeOrRegionFile_conditional"> <param name="chromosomeOrRegionFile_selector" type="select" label="List of chromosomes or a BED file containg regions"> <option value="optionChromosomes">Chromosomes</option> <option value="optionRegionFile" selected="True">Region BED file</option> </param> <when value="optionChromosomes"> <repeat name="chromosomeOrder" min="0" title="Chromosomes to keep / remove / mask" help="The selected option will be applied on the selected chromosomes."> <param name="chromosome" type="text"> <validator type="empty_field" /> </param> </repeat> </when> <when value="optionRegionFile"> <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered" help="Should contain the regions which should be kept, removed or masked." /> </when> </conditional> <param name="interIntra_selector" type="select" label="Remove inter- or intra chromosomal regions"> <option value="keep" selected="True">Do not apply</option> <option value="inter">Remove inter-chromosomal contacts</option> <option value="intra">Remove intra-chromosomal contacts</option> </param> </inputs> <outputs> <data name="outFileName" from_work_dir="matrix" format="h5"> <change_format> <when input="matrix_h5_cooler.ext" value="cool" format="cool" /> </change_format> </data> </outputs> <tests> <test expect_num_outputs="1"> <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> <param name="action_selector" value="keep" /> <conditional name="chromosomeOrRegionFile_conditional"> <param name="chromosomeOrRegionFile_selector" value="optionChromosomes" /> <repeat name="chromosomeOrder"> <param name="chromosome" value="chrX" /> <param name="chromosome" value="chr3R" /> </repeat> </conditional> <output name="outFileName" ftype="h5"> <assert_contents> <has_h5_keys keys="intervals,matrix" /> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> <param name="action_selector" value="mask" /> <conditional name="chromosomeOrRegionFile_conditional"> <param name="chromosomeOrRegionFile_selector" value="optionRegionFile" /> <param name="regions" value="regions.bed" /> </conditional> <output name="outFileName" ftype="h5"> <assert_contents> <has_h5_keys keys="intervals,matrix,nan_bins" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ Adjust of the Hi-C matrix ========================= This tool is able to remove, keep or mask given regions of a Hi-C interaction matrix, including entire chromosomes. _________________ | 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>