diff mismatch_profile.xml @ 13:a7f9084572fe draft

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

--- a/mismatch_profile.xml	Sat Dec 18 19:40:16 2021 +0000
+++ b/mismatch_profile.xml	Sat Dec 10 11:21:47 2022 +0000
@@ -1,11 +1,11 @@
-<tool id="rseqc_mismatch_profile" name="Mismatch Profile" version="@TOOL_VERSION@">
+<tool id="rseqc_mismatch_profile" name="Mismatch Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>
      calculates the distribution of mismatches across reads
     </description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
 
     <expand macro="requirements" />
 
@@ -14,7 +14,8 @@
     <version_command><![CDATA[mismatch_profile.py --version]]></version_command>
 
     <command><![CDATA[
-        mismatch_profile.py -i '${input}' -o output -l ${readlength} -n ${readnum} -q ${mapq}
+        @BAM_SAM_INPUTS@
+        mismatch_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq}
         ]]>
     </command>
 
@@ -35,7 +36,7 @@
     <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.mismatch_profile.pdf" compare="sim_size" />
             <output name="outputxls" file="output.mismatch_profile.xls"/>