Mercurial > repos > bgruening > hicexplorer_hicadjustmatrix
view hicAdjustMatrix.xml @ 1:ea297a9c6f11 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
author | bgruening |
---|---|
date | Wed, 05 Feb 2020 19:49:01 -0500 |
parents | 74b3932d0836 |
children | cc52e4ded146 |
line wrap: on
line source
<tool id="hicexplorer_hicadjustmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> <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 && 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> </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> <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> <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. _________________ | 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>