# HG changeset patch
# User iuc
# Date 1656353666 0
# Node ID 0564602cd4dfe7b0c4d51056027504815063420f
# Parent  790d4c1f2ea0c458aeb9179091cd31912742615b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6

diff -r 790d4c1f2ea0 -r 0564602cd4df lr.xml
--- a/lr.xml	Tue Dec 14 19:03:14 2021 +0000
+++ b/lr.xml	Mon Jun 27 18:14:26 2022 +0000
@@ -10,13 +10,13 @@
     <command detect_errors="exit_code"><![CDATA[
 ## initialize
 @BAM@
-
+@FASTA@
 ## run
 delly lr
 ## generic options
 --svtype $generic.svtype
 --technology $generic.technology
---genome '$generic.genome'
+--genome genome.fa
 #if $generic.exclude
     --exclude '$generic.exclude'
 #end if
@@ -99,12 +99,12 @@
             </section>
             <output name="out_bcf">
                 <assert_contents>
-                    <has_size value="1184" delta="10"/>
+                    <has_size value="1127" delta="10"/>
                 </assert_contents>
             </output>
             <output name="out_vcf">
                 <assert_contents>
-                    <has_size value="3661" delta="10"/>
+                    <has_n_lines n="46"/>
                     <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
                 </assert_contents>
             </output>
@@ -120,7 +120,7 @@
             </section>
             <output name="out_bcf">
                 <assert_contents>
-                    <has_size value="1189" delta="10"/>
+                    <has_size value="1131" delta="10"/>
                 </assert_contents>
             </output>
             <output name="out_log">
@@ -130,7 +130,7 @@
             </output>
             <output name="out_vcf">
                 <assert_contents>
-                    <has_size value="3667" delta="10"/>
+                    <has_n_lines valuen="42"/>
                 </assert_contents>
             </output>
         </test>
@@ -146,7 +146,7 @@
             </section>
             <output name="out_bcf">
                 <assert_contents>
-                    <has_size value="1186" delta="10"/>
+                    <has_size value="1127" delta="10"/>
                 </assert_contents>
             </output>
             <output name="out_dump">
@@ -161,7 +161,7 @@
             </output>
             <output name="out_vcf">
                 <assert_contents>
-                    <has_size value="3661" delta="10"/>
+                    <has_n_lines n="46"/>
                 </assert_contents>
             </output>
         </test>
@@ -195,7 +195,7 @@
             </section>
             <output name="out_bcf">
                 <assert_contents>
-                    <has_size value="1182" delta="10"/>
+                    <has_size value="1127" delta="10"/>
                 </assert_contents>
             </output>
             <output name="out_dump">
@@ -210,7 +210,7 @@
             </output>
             <output name="out_vcf">
                 <assert_contents>
-                    <has_size value="3661" delta="10"/>
+                    <has_n_lines n="46"/>
                     <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
                 </assert_contents>
             </output>
@@ -227,7 +227,7 @@
             </section>
             <output name="out_vcf">
                 <assert_contents>
-                    <has_size value="3661" delta="10"/>
+                    <has_n_lines n="46"/>
                     <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
                 </assert_contents>
             </output>
@@ -244,7 +244,7 @@
             </section>
             <output name="out_bcf">
                 <assert_contents>
-                    <has_size value="1182" delta="10"/>
+                    <has_size value="1127" delta="10"/>
                 </assert_contents>
             </output>
         </test>
diff -r 790d4c1f2ea0 -r 0564602cd4df macros.xml
--- a/macros.xml	Tue Dec 14 19:03:14 2021 +0000
+++ b/macros.xml	Mon Jun 27 18:14:26 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.'