# HG changeset patch
# User iuc
# Date 1638016334 0
# Node ID 92ec40abcdcfb589ea645064ec52b0b4f7f50cc5
# Parent c147e3a105738646fbfc8560e468545953ad4276
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit c5ded4208dd70e88596ddc725795a2401773f02d"
diff -r c147e3a10573 -r 92ec40abcdcf macros.xml
--- a/macros.xml Tue Sep 28 16:12:02 2021 +0000
+++ b/macros.xml Sat Nov 27 12:32:14 2021 +0000
@@ -50,23 +50,56 @@
#end for
]]>
&2 &&
+ gzip -dc \$reffa > reference.fa &&
+ reffa="reference.fa" &&
+ samtools faidx \$reffa;
+ }
+ } &&
+ #end if
+ reffai=\$reffa.fai &&
#elif $addref_cond.addref_select == "cached":
- #set reffa=str($addref_cond.ref.fields.path)
- #set reffai=str($addref_cond.ref.fields.path)+".fai"
+ ## in case of cached the absolute path is used which allows to read
+ ## a cram file without specifying the reference
+ reffa='${addref_cond.ref.fields.path}' &&
+ reffai=\$reffa.fai &&
#else
- #set reffa=None
- #set reffai=None
+ #set use_ref=False
#end if
]]>
diff -r c147e3a10573 -r 92ec40abcdcf samtools_calmd.xml
--- a/samtools_calmd.xml Tue Sep 28 16:12:02 2021 +0000
+++ b/samtools_calmd.xml Sat Nov 27 12:32:14 2021 +0000
@@ -18,7 +18,7 @@
-b
-@ \$addthreads
'$input'
- '$reffa'
+ "\$reffa"
> '$calmd_output'
]]>