# HG changeset patch
# User iuc
# Date 1660555046 0
# Node ID 41e36c99a00806282885851e642362d3d85ebbd3
# Parent 595ae1ba934ae8ede5cd266208146ee5ec9f8796
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 5cb103832529f17e5c72e7f122758c13519fbe5e
diff -r 595ae1ba934a -r 41e36c99a008 macros.xml
--- a/macros.xml Tue Sep 28 16:13:23 2021 +0000
+++ b/macros.xml Mon Aug 15 09:17:26 2022 +0000
@@ -5,7 +5,7 @@
- 1.13
+ 1.15.1
20.05
&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
]]>
-
+
@HELP@
diff -r 595ae1ba934a -r 41e36c99a008 samtools_fixmate.xml
--- a/samtools_fixmate.xml Tue Sep 28 16:13:23 2021 +0000
+++ b/samtools_fixmate.xml Mon Aug 15 09:17:26 2022 +0000
@@ -1,4 +1,4 @@
-
+
fill mate coordinates, ISIZE and mate related flags
macros.xml