# HG changeset patch
# User iuc
# Date 1655884103 0
# Node ID 887e02a45734feb2152fbe55045e7cb43dfba8ae
# Parent  8c440c3002bc868419d6e2fbaee0e3ff625381e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 84db51c96845854eb42c1a9949e4b79316b41925

diff -r 8c440c3002bc -r 887e02a45734 samtools_markdup.xml
--- a/samtools_markdup.xml	Sun Dec 19 15:56:46 2021 +0000
+++ b/samtools_markdup.xml	Wed Jun 22 07:48:23 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@" profile="@PROFILE@" >
+<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" >
     <description>marks duplicate alignments</description>
     <macros>
         <import>macros.xml</import>
@@ -19,6 +19,12 @@
     ln -s '$bamfile' coordsort.sam &&
 #end if
 
+## copy fasta reference if needed
+## because samtools will try to write a .fai file next to it
+#if $output_options.output_format.select_oformat == "CRAM"
+    ln -s '$output_options.output_format.ref_file' ref_file.fa &&
+#end if
+
 samtools markdup
 
 -@ \$addthreads
@@ -39,7 +45,7 @@
 #end if
 -O $output_options.output_format.select_oformat
 #if $output_options.output_format.select_oformat == "CRAM"
-    --reference '$output_options.output_format.ref_file'
+    --reference ref_file.fa
 #end if
 coordsort.sam
 '$output'