Mercurial > repos > iuc > delly_cnv

diff cnv.xml @ 2:8ad49c4272ea draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
author iuc
date Mon, 27 Jun 2022 18:18:05 +0000
parents 56781a718729
children
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--- a/cnv.xml	Tue Dec 14 19:06:35 2021 +0000
+++ b/cnv.xml	Mon Jun 27 18:18:05 2022 +0000
@@ -8,12 +8,16 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
+@SINGLE_BAM@
+@FASTA@
+ln -s '$generic.mappability' mappability.fa &&
+
 ## run
 delly cnv
 ## generic options
---genome '$generic.genome'
+--genome genome.fa
 --quality '$generic.quality'
---mappability '$generic.mappability'
+--mappability mappability.fa
 --ploidy $generic.ploidy
 --outfile 'result.bcf'
 --covfile 'result.gz'
@@ -46,7 +50,7 @@
 --percentile $gc.percentile
 $gc.nowindowselection
 ## input
-'$input'
+'input.bam'
 
 ## postprocessing
 @LOG@
@@ -162,7 +166,7 @@
             </section>
             <output name="out_cnv">
                 <assert_contents>
-                    <has_size value="700" delta="10"/>
+                    <has_size value="645" delta="10"/>
                 </assert_contents>
             </output>
             <output name="out_coverage">