# HG changeset patch
# User iuc
# Date 1656353699 0
# Node ID 1ddff01fee0b291b0592427c7b86f9c85bfb9280
# Parent  259b3fabd7b0f66208e36131152e0ab0d3aa4a3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6

diff -r 259b3fabd7b0 -r 1ddff01fee0b cnv.xml
--- a/cnv.xml	Tue Dec 14 19:03:45 2021 +0000
+++ b/cnv.xml	Mon Jun 27 18:14:59 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">
diff -r 259b3fabd7b0 -r 1ddff01fee0b macros.xml
--- a/macros.xml	Tue Dec 14 19:03:45 2021 +0000
+++ b/macros.xml	Mon Jun 27 18:14:59 2022 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">0.9.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
@@ -23,12 +23,20 @@
     </xml>
     <!-- command -->
 
+    <token name="@SINGLE_BAM@"><![CDATA[
+ln -s '$input' 'input.bam' &&
+ln -s '$input.metadata.bam_index' 'input.bam.bai' &&
+    ]]></token>
     <token name="@BAM@"><![CDATA[
 #for $i, $current in enumerate($input)
     ln -s '${current}' 'input_${i}.bam' &&
     ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' &&
 #end for
     ]]></token>
+    <!-- fasta needs to be linked, because .fai file is created -->
+    <token name="@FASTA@"><![CDATA[
+ln -s '$generic.genome' genome.fa &&
+    ]]></token>
     <token name="@DUMP@"><![CDATA[
 #if 'dump' in $oo.out
     && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'