diff RNA_fragment_size.xml @ 13:a7f9084572fe draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a

--- a/RNA_fragment_size.xml	Sat Dec 18 19:40:16 2021 +0000
+++ b/RNA_fragment_size.xml	Sat Dec 10 11:21:47 2022 +0000
@@ -1,11 +1,11 @@
-<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>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
 
     <expand macro="requirements" />
 
@@ -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>