--- a/ribotaper_part2_create_metaplots.xml	Wed Nov 30 16:57:07 2016 -0500
+++ b/ribotaper_part2_create_metaplots.xml	Fri Jun 03 20:17:28 2022 +0000
@@ -1,19 +1,18 @@
-<tool id="ribotaper_create_metaplots" name="ribotaper part 2: metagene analysis for P-sites definition" version="0.1.0">
-    <requirements>
-            <requirement type="package" version="1.3.1a">ribotaper</requirement>
-    </requirements>
+<tool id="ribotaper_create_metaplots" name="ribotaper part 2: metagene analysis for P-sites definition" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile='20.01'>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro='bio_tools'/>
+    <expand macro='requirements'/>
     <stdio>
         <exit_code range="1:" />
     </stdio>
-
     <command><![CDATA[
         create_metaplots.bash
             "$ribo_bam"
             "$start_stops_FAR"
             "metagene"
-
         &&
-
         find "metaplots"
             "-name"
             "metagene*.pdf"
@@ -24,18 +23,17 @@
             "-q"
             "-sDEVICE=pdfwrite"
             "-sOutputFile=merged_metagene.pdf"
-
     ]]></command>
     <inputs>
-        <param name="ribo_bam" type="data" format="bam" label="ribo_bam" help="Ribo-seq alignment file in BAM format."/>
-        <param name="start_stops_FAR" type="data" format="bed" label="start_stops_FAR" help="Please run 'ribotaper part 1' to generate the table."/>
+        <param name="ribo_bam" type="data" format="bam" label="Ribo-seq alignment file" help="Ribo-seq alignment file in BAM format."/>
+        <param name="start_stops_FAR" type="data" format="bed" label="Start_stops FAR" help="Please run 'ribotaper part 1' to generate the table."/>
     </inputs>
     <outputs>
-        <data name="output1" format="pdf" from_work_dir="merged_metagene.pdf" label="Metagene analysis results for P-sites definition (figures)"/>
-        <data name="output2" format="tabular" from_work_dir="metagene" label="Metagene analysis results for P-sites definition (table)"/>
+        <data name="output1" format="pdf" from_work_dir="merged_metagene.pdf" label="${tool.name} on ${on_string}: Metagene analysis results for P-sites definition (figures)"/>
+        <data name="output2" format="tabular" from_work_dir="metagene" label="${tool.name} on ${on_string}: Metagene analysis results for P-sites definition (table)"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="ribo_bam" value="test_ribo.bam" ftype="bam"/>
             <param name="start_stops_FAR" value="annotation_path/start_stops_FAR.bed"  ftype="bed"/>
             <output name="output2" file="metagene"/>
@@ -87,7 +85,5 @@
 for running ``ribotaper part 3``, ribosome profiling.
 
 ]]></help>
-    <citations>
-        <citation type="doi">10.1038/nmeth.3688</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>