# HG changeset patch
# User bgruening
# Date 1580950559 18000
# Node ID 3f529510975e98dd8f845c3a895e42c6a538f862
# Parent ae9cc6dbfaca17ffc2db9372fb3561dd31dc07a4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
diff -r ae9cc6dbfaca -r 3f529510975e hicTransform.xml
--- a/hicTransform.xml Mon Dec 16 15:41:36 2019 -0500
+++ b/hicTransform.xml Wed Feb 05 19:55:59 2020 -0500
@@ -10,7 +10,16 @@
ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
@BINARY@ --matrix 'matrix.$matrix_h5_cooler.ext'
--method $method_selector
+ #if $ligation_factor:
+ $ligation_factor
+ #end if
+ $perChromosome
+ #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomeOrder ])
+ #if chroms:
+ --chromosomes $chroms
+ #end if
--outFileName 'matrix.$matrix_h5_cooler.ext'
+
&& mv 'matrix.$matrix_h5_cooler.ext' matrix
]]>
@@ -18,12 +27,19 @@
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@@ -35,7 +51,18 @@
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