diff FPKM_count.xml @ 13:a7f9084572fe draft

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

--- a/FPKM_count.xml	Sat Dec 18 19:40:16 2021 +0000
+++ b/FPKM_count.xml	Sat Dec 10 11:21:47 2022 +0000
@@ -1,10 +1,11 @@
-<tool id="rseqc_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@.1">
+<tool id="rseqc_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>calculates raw read count, FPM, and FPKM for each gene</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
 
+    <expand macro="bio_tools"/>
+
     <expand macro="requirements" />
 
     <expand macro="stdio" />
@@ -12,9 +13,8 @@
     <version_command><![CDATA[FPKM_count.py --version]]></version_command>
 
     <command><![CDATA[
-        ln -sf '${input}' 'local_input.bam' &&
-        ln -sf '${input.metadata.bam_index}' 'local_input.bam.bai' &&
-        FPKM_count.py -i 'local_input.bam' -o output -r '${refgene}'
+        @BAM_SAM_INPUTS@
+        FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}'
 
         #if str($strand_type.strand_specific) == "pair"
             -d