# HG changeset patch
# User iuc
# Date 1657091210 0
# Node ID 6f3e5e591f0bc88a0dab884e6d61695252b0698f
# Parent  9cba5b855260aed980770866b697615704350d2e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637

diff -r 9cba5b855260 -r 6f3e5e591f0b irissv.xml
--- a/irissv.xml	Mon May 17 17:29:06 2021 +0000
+++ b/irissv.xml	Wed Jul 06 07:06:50 2022 +0000
@@ -1,5 +1,4 @@
-<?xml version="1.0"?>
-<tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>Refine insertion sequences</description>
     <macros>
         <import>macros.xml</import>
@@ -8,13 +7,16 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
 
-    <command detect_errors="exit_code"><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
     @REF_FASTA@
 
+    ln -s '$in_bam' reads.bam &&
+    ln -s '$in_bam.metadata.bam_index' 'reads.bam.bai' &&
+
     iris
         genome_in=reference
         vcf_in='${in_vcf}'
-        reads_in='${in_bam}'
+        reads_in='reads.bam'
         vcf_out='${out_vcf}'
         threads=\${GALAXY_SLOTS:-4}
         padding_before='${padding_before}'