diff filter.xml @ 1:9919057a466c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"

--- a/filter.xml	Mon Sep 28 07:44:40 2020 +0000
+++ b/filter.xml	Thu Oct 29 20:50:57 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy0" profile="18.01">
+<tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
     <description>somatic or germline structural variants</description>
     <macros>
         <import>macros.xml</import>
@@ -42,19 +42,15 @@
 'sample.bcf.gz' ## input
 
 ## postprocessing
-#if 'log' in $oo.out
-    |& tee 'log.txt'
-#end if
-#if 'vcf' in $oo.out
-    && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
-#end if
+@LOG@
+@VCF@
     ]]></command>
     <inputs>
         <expand macro="samples" format="bcf,vcf" multiple="false" label="Select file"/>
         <section name="generic" title="Generic options" expanded="true">
             <param argument="--altaf" type="float" value="0.2" min="0.0" max="1.0" label="Set minimum fractional ALT support"/>
-            <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/>
-            <param argument="--maxsize" type="integer" value="500000000" label="Set maximum SV size"/>
+            <expand macro="minsize"/>
+            <expand macro="maxsize" default="500000000"/>
             <param argument="--ratiogeno" type="float" value="0.75" min="0.0" max="1.0" label="Set minimum fraction of genotyped samples"/>
             <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
         </section>