Mercurial > repos > jackcurragh > ribogalaxy_samtools_sort_transcriptome

changeset 5:21eceda8a1ae draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jackcurragh
date Tue, 07 Jun 2022 12:32:37 +0000
parents 9445a308fb7e
children
files samtools_sort_transcriptome/samtools_sort.xml
diffstat 1 files changed, 2 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/samtools_sort_transcriptome/samtools_sort.xml	Tue Jun 07 11:33:01 2022 +0000
+++ b/samtools_sort_transcriptome/samtools_sort.xml	Tue Jun 07 12:32:37 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_transcriptome_sort" name="Samtools sort" version="2.0.5" profile="@PROFILE@">
+<tool id="samtools_transcriptome_sort" name="Samtools sort" version="2.0.6" profile="@PROFILE@">
     <description>Sort Alignment Files (SAM/BAM)</description>
     <macros>
         <import>macros.xml</import>
@@ -22,26 +22,7 @@
             '${input1}'
              > '${output1}'
     ]]>
-    <!-- <![CDATA[
-        @ADDTHREADS@
-	@ADDMEMORY@
-        samtools sort
-            -@ \$addthreads
-            -m \$addmemory"M"
-            ###if str(compression):
-            ##    -l '$compression'
-            ###end if
-            $prim_key_cond.prim_key_select
-            #if $prim_key_cond.prim_key_select == '-t':
-                $prim_key_cond.tag
-                $prim_key_cond.sec_key_select
-            #end if
-            $minhash
-            -O bam
-            -T "\${TMPDIR:-.}"
-            '${input1}'
-             > '${output1}'
-    ]]>--></command>
+    </command>
     <inputs>
         <param name="input1" type="data" format="sam,unsorted.bam,cram" label="BAM File" />
         <conditional name="prim_key_cond">