diff lr.xml @ 1:d5124d5c8131 draft

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

--- a/lr.xml	Mon Sep 28 07:45:41 2020 +0000
+++ b/lr.xml	Thu Oct 29 20:51:54 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="delly_lr" name="Delly long-read (lr)" version="@TOOL_VERSION@+galaxy0" profile="18.01">
+<tool id="delly_lr" name="Delly long-read (lr)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
     <description>optimized calling and genotyping of 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 lr
@@ -26,6 +23,7 @@
 ## discovery options
 --mapqual $discovery.mapqual
 --minclip $discovery.minclip
+--min-clique-size $discovery.mincliquesize
 --minrefsep $discovery.minrefsep
 --maxreadsep $discovery.maxreadsep
 ## genotyping options
@@ -42,15 +40,9 @@
 #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"/>
@@ -66,8 +58,9 @@
         <section name="discovery" title="Discovery options" expanded="true">
             <param argument="--mapqual" type="integer" value="1" label="Set minimum mapping quality"/>
             <expand macro="minclip"/>
-            <expand macro="minrefsep"/>
-            <expand macro="maxreadsep"/>
+            <expand macro="mincliquesize"/>
+            <expand macro="minrefsep" defaut="30"/>
+            <expand macro="maxreadsep" defaut="75"/>
         </section>
         <section name="genotyping" title="Genotyping options" expanded="true">
             <expand macro="vcffile"/>
@@ -181,6 +174,7 @@
                 <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>
@@ -285,15 +279,15 @@
 
 @WID@
 
-Delly *lr* uses the long-read SV discovery mode.
+Delly *long-read (lr)* uses the long-read SV discovery mode.
 
 **Input**
 
-Delly *lr* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a VCF/BCF file for genotyping can be applied.
+Delly *long-read (lr)* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a VCF/BCF file for genotyping can be applied.
 
 **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