diff insertion_profile.xml @ 13:a7f9084572fe draft

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

--- a/insertion_profile.xml	Sat Dec 18 19:40:16 2021 +0000
+++ b/insertion_profile.xml	Sat Dec 10 11:21:47 2022 +0000
@@ -1,12 +1,13 @@
-<tool id="rseqc_insertion_profile" name="Insertion Profile" version="@TOOL_VERSION@">
+<tool id="rseqc_insertion_profile" name="Insertion Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>
      calculates the distribution of inserted nucleotides across reads
     </description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
 
+    <expand macro="bio_tools"/>
+
     <expand macro="requirements" />
 
     <expand macro="stdio" />
@@ -14,12 +15,13 @@
     <version_command><![CDATA[insertion_profile.py --version]]></version_command>
 
     <command><![CDATA[
-        insertion_profile.py -i '${input}' -o output -q ${mapq} -s "${layout}"
+        @BAM_SAM_INPUTS@
+        insertion_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}"
         ]]>
     </command>
 
     <inputs>
-        <expand macro="bam_param" />
+        <expand macro="bam_sam_param" />
         <expand macro="mapq_param" />
         <expand macro="layout_param" />
         <expand macro="rscript_output_param" />