Mercurial > repos > artbio > lumpy_smoove

diff lumpy_smoove.xml @ 7:8b0005fdfd04 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
author artbio
date Sun, 18 Apr 2021 17:08:22 +0000
parents ad8853ee9909
children b4dec06d8fc6
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line diff
--- a/lumpy_smoove.xml	Sun Feb 14 23:59:42 2021 +0000
+++ b/lumpy_smoove.xml	Sun Apr 18 17:08:22 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy6">
+<tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy7">
     <description>find structural variants using the smoove workflow</description>
     <macros>
         <import>macro_lumpy_smoove.xml</import>
@@ -25,7 +25,6 @@
             ln -s $sample ${sample.element_identifier}.bam &&
             ln -f -s $sample.metadata.bam_index ${sample.element_identifier}.bam.bai &&
         #end for
-    ls -la &&
     #end if
    
     smoove call --name output
@@ -39,8 +38,7 @@
             --removepr
        #end if
            *.bam &&
-    ls -latr &&
-    gunzip output-smoove.genotyped.vcf.gz
+    gunzip -c output-smoove.genotyped.vcf.gz > $vcf_call
 
     ]]></command>
     <inputs>
@@ -82,7 +80,7 @@
    </inputs>
 
     <outputs>
-        <data format="vcf" name="vcf_call" label="lumpy-smoove Variant Calling" from_work_dir="./output-smoove.genotyped.vcf" />
+        <data format="vcf" name="vcf_call" label="lumpy-smoove Variant Calling" />
     </outputs>
 
     <tests>