diff RPKM_saturation.xml @ 60:1421603cc95b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d

--- a/RPKM_saturation.xml	Sat Dec 18 19:41:19 2021 +0000
+++ b/RPKM_saturation.xml	Sat Nov 26 15:19:14 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@TOOL_VERSION@.2">
+<tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>
     <expand macro="bio_tools"/>
     <macros>
@@ -12,7 +12,8 @@
     <version_command><![CDATA[RPKM_saturation.py --version]]></version_command>
 
     <command><![CDATA[
-        RPKM_saturation.py -i '${input}' -o output -r '${refgene}'
+        @BAM_SAM_INPUTS@
+        RPKM_saturation.py -i 'input.${extension}' -o output -r '${refgene}'
 
         #if str($strand_type.strand_specific) == "pair"
             -d
@@ -37,7 +38,7 @@
     ]]></command>
 
     <inputs>
-        <expand macro="bam_param" />
+        <expand macro="bam_sam_param" />
         <expand macro="refgene_param" />
         <expand macro="strand_type_param" />
         <param name="percentileFloor" type="integer" value="5" label="Begin sampling from this percentile (default=5)" help="(--percentile-floor)"/>