Mercurial > repos > bgruening > hicexplorer_hictransform
comparison hicTransform.xml @ 17:27fe5cd1729c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
| author | iuc |
|---|---|
| date | Mon, 01 Jul 2024 19:54:05 +0000 |
| parents | f36828ebdc54 |
| children |
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| 16:f36828ebdc54 | 17:27fe5cd1729c |
|---|---|
| 1 <tool id="hicexplorer_hictransform" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> | 1 <tool id="hicexplorer_hictransform" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 2 <description>transform a matrix to obs/exp, pearson and covariance matrices</description> | 2 <description>transform a matrix to obs/exp, pearson and covariance matrices</description> |
| 3 <macros> | 3 <macros> |
| 4 <token name="@BINARY@">hicTransform</token> | 4 <token name="@BINARY@">hicTransform</token> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 16 $perChromosome | 16 $perChromosome |
| 17 #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomeOrder ]) | 17 #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomeOrder ]) |
| 18 #if chroms: | 18 #if chroms: |
| 19 --chromosomes $chroms | 19 --chromosomes $chroms |
| 20 #end if | 20 #end if |
| 21 --outFileName 'matrix.$matrix_h5_cooler.ext' | 21 --outFileName 'out_matrix.$matrix_h5_cooler.ext' |
| 22 | 22 |
| 23 && mv 'matrix.$matrix_h5_cooler.ext' matrix | 23 && mv 'out_matrix.$matrix_h5_cooler.ext' matrix |
| 24 ]]> | 24 ]]> |
| 25 </command> | 25 </command> |
| 26 <inputs> | 26 <inputs> |
| 27 <expand macro="matrix_h5_cooler_macro" /> | 27 <expand macro="matrix_h5_cooler_macro" /> |
| 28 <param name="method_selector" type="select" label="Choose method to apply"> | 28 <param name="method_selector" type="select" label="Choose method to apply"> |