Mercurial > repos > nilesh > rseqc

diff deletion_profile.xml @ 13:a7f9084572fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
author iuc
date Sat, 10 Dec 2022 11:21:47 +0000
parents 57fad5deeb8e
children b21f0167e197
line wrap: on
line diff
--- a/deletion_profile.xml	Sat Dec 18 19:40:16 2021 +0000
+++ b/deletion_profile.xml	Sat Dec 10 11:21:47 2022 +0000
@@ -1,12 +1,13 @@
-<tool id="rseqc_deletion_profile" name="Deletion Profile" version="@TOOL_VERSION@">
+<tool id="rseqc_deletion_profile" name="Deletion Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>
      calculates the distributions of deleted 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" />
@@ -14,7 +15,8 @@
     <version_command><![CDATA[deletion_profile.py --version]]></version_command>
 
     <command><![CDATA[
-        deletion_profile.py -i '${input}' -o output -l ${readlength} -n ${readnum} -q ${mapq}
+        @BAM_SAM_INPUTS@
+        deletion_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq}
         ]]>
     </command>
 
@@ -35,7 +37,7 @@
     <tests>
         <test>
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
-            <param name="readlength" value="101" />
+            <param name="read_align_length" value="101" />
             <param name="rscript_output" value="true" />
             <output name="outputpdf" file="output.deletion_profile.pdf" compare="sim_size" />
             <output name="outputxls" file="output.deletion_profile.txt" />