--- a/call.xml	Mon Sep 28 07:45:21 2020 +0000
+++ b/call.xml	Thu Oct 29 20:50:39 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="delly_call" name="Delly call" version="@TOOL_VERSION@+galaxy0" profile="18.01">
+<tool id="delly_call" name="Delly call" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
     <description>and genotype structural variants</description>
     <macros>
         <import>macros.xml</import>
@@ -8,10 +8,7 @@
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
 ## initialize
-#for $i, $current in enumerate($samples)
-    ln -s '${current}' 'sample_${i}.bam' &&
-    ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' &&
-#end for
+@BAM@
 
 ## run
 delly call
@@ -27,6 +24,7 @@
 --qual-tra $discovery.qualtra
 --mad-cutoff $discovery.madcutoff
 --minclip $discovery.minclip
+--min-clique-size $discovery.mincliquesize
 --minrefsep $discovery.minrefsep
 --maxreadsep $discovery.maxreadsep
 ## genotyping options
@@ -43,15 +41,9 @@
 #end for
 
 ## 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
-#if 'dump' in $oo.out
-    && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
-#end if
+@LOG@
+@VCF@
+@DUMP@
     ]]></command>
     <inputs>
         <expand macro="samples"/>
@@ -65,6 +57,7 @@
             <param name="qualtra" type="integer" value="20" label="Set minimum PE quality for translocation" help="(--qual-tra)"/>
             <param name="madcutoff" type="integer" value="9" label="Set insert size cutoff" help="median+s*MAD, deletions only (--mad-cutoff)"/>
             <expand macro="minclip"/>
+            <expand macro="mincliquesize"/>
             <expand macro="minrefsep"/>
             <expand macro="maxreadsep"/>
         </section>
@@ -179,6 +172,7 @@
                 <param name="qualtra" value="19"/>
                 <param name="madcutoff" value="8"/>
                 <param name="minclip" value="24"/>
+                <param name="mincliquesize" value="1"/>
                 <param name="minrefsep" value="24"/>
                 <param name="maxreadsep" value="39"/>
             </section>
@@ -279,7 +273,7 @@
 
 **Output**
 
-The output is available in BCF and VCF format. Additionally a output file for SV-reads is provided.
+The output is available in BCF and VCF format. Additionally an output file for SV-reads is provided.
 
 .. class:: infomark