Mercurial > repos > nilesh > rseqc

diff RNA_fragment_size.xml @ 60:1421603cc95b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
author iuc
date Sat, 26 Nov 2022 15:19:14 +0000
parents dbedfc5f5a3c
children 5968573462fa
line wrap: on
line diff
--- a/RNA_fragment_size.xml	Sat Dec 18 19:41:19 2021 +0000
+++ b/RNA_fragment_size.xml	Sat Nov 26 15:19:14 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@TOOL_VERSION@.1">
+<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>
      calculates the fragment size for each gene/transcript
     </description>
@@ -14,9 +14,8 @@
     <version_command><![CDATA[RNA_fragment_size.py --version]]></version_command>
 
     <command><![CDATA[
-        ln -sf '${input}' 'input.bam' &&
-        ln -sf '$input.metadata.bam_index' 'input.bam.bai' &&
-        RNA_fragment_size.py -i 'input.bam' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}'
+        @BAM_SAM_INPUTS@
+        RNA_fragment_size.py -i 'input.${extension}' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}'
         ]]>
     </command>