--- a/ribotaper_part3_main.xml	Wed Nov 30 16:57:07 2016 -0500
+++ b/ribotaper_part3_main.xml	Fri Jun 03 20:17:28 2022 +0000
@@ -1,49 +1,62 @@
-<tool id="ribotaper_ribosome_profiling" name="ribotaper part 3: ribosome profiling" version="0.1.0">
-    <requirements>
-            <requirement type="package" version="1.3.1a">ribotaper</requirement>
-    </requirements>
+<tool id="ribotaper_ribosome_profiling" name="ribotaper part 3: ribosome profiling" 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[
-        tar
-            "xzvf"
-            "$annotation_path"
-
-        &&
-
+        #if $annotation_path.is_of_type("tgz")
+            tar -xzvf '${annotation_path}' &&
+        #else
+             tar -xvf '${annotation_path}' &&
+        #end if
         Ribotaper.sh
-            "$ribo_bam"
-            "$rna_bam"
-            "annotation_path"
-            "$read_lenghts_ribo"
-            "$cutoff"
-            "\${GALAXY_SLOTS:-12}"
-
+            '${ribo_bam}'
+            '${rna_bam}'
+            './annotation_path'
+            '${read_lenghts_ribo}'
+            '${cutoff}'
+            \${GALAXY_SLOTS:-12}
     ]]></command>
     <inputs>
-        <param name="annotation_path" type="data" format="tar" label="annotation_path" help="Please run 'ribotaper part 1' to generate the archive."/>
-        <param name="ribo_bam" type="data" format="BAM" label="ribo_bam" help="Ribo-seq alignment file in BAM format."/>
-        <param name="rna_bam" type="data" format="BAM" label="rna_bam" help="RNA-seq alignment file in BAM format."/>
+        <param name="annotation_path" type="data" format="tgz,tar" label="Annotation path" help="Please run 'ribotaper part 1' to generate the archive."/>
+        <param name="ribo_bam" type="data" format="BAM" label="Ribo-seq alignment file" help="Ribo-seq alignment file in BAM format."/>
+        <param name="rna_bam" type="data" format="BAM" label="RNA-seq alignment file" help="RNA-seq alignment file in BAM format."/>
         <param name="read_lenghts_ribo" type="text" value="26,28,29"  label="Read length" help="Read lengths, comma-separated values, which are used for P-site calculation. Example, 26,28,29.
-        Please run 'ribotaper part 2' to deterimine appropriate values."/>
+            Please run 'ribotaper part 2' to deterimine appropriate values.">
+            <sanitizer invalid_char="">
+                <valid initial="string.digits">
+                    <add value="," />
+                </valid>
+            </sanitizer>
+            <validator type="regex">[0-9,]+</validator>
+        </param>
         <param name="cutoff" type="text" value="9,12,12"  label="Cutoff" help="Cutoffs, comma-separated values, which are used for P-sites calculation. Example, 9,12,12.
-        Please run 'ribotaper part 2' to deterimine appropriate values."/>
+            Please run 'ribotaper part 2' to deterimine appropriate values.">
+            <sanitizer invalid_char="">
+                <valid initial="string.digits">
+                    <add value="," />
+                </valid>
+            </sanitizer>
+            <validator type="regex">[0-9,]+</validator>
+        </param>
     </inputs>
     <outputs>
-        <data name="output1" format="pdf" from_work_dir="quality_check_plots.pdf" label="QC plots"/>
-        <data name="output2" format="tabular" from_work_dir="ORFs_genes_found" label="Summary of translated ORFs"/>
-        <data name="output3" format="tabular" from_work_dir="ORFs_max" label="Translated ORFs (max)"/>
-        <data name="output4" format="tabular" from_work_dir="ORFs_max_filt" label="Translated ORFs (max_filt)"/>
-        <data name="output5" format="bed" from_work_dir="translated_ORFs_sorted.bed" label="Translated ORFs (sorted)"/>
-        <data name="output6" format="bed" from_work_dir="translated_ORFs_filtered_sorted.bed" label="Translated ORFs (filtered/sorted)"/>
-        <data name="output7" format="fasta" from_work_dir="protein_db_max.fasta" label="Protein DB"/>
-        <data name="output8" format="pdf" from_work_dir="Final_ORF_results.pdf" label="ORF categories (length/coverage)"/>
+        <data name="output1" format="pdf" from_work_dir="quality_check_plots.pdf" label="${tool.name} on ${on_string}: QC plots"/>
+        <data name="output2" format="tabular" from_work_dir="ORFs_genes_found" label="${tool.name} on ${on_string}: Summary of translated ORFs"/>
+        <data name="output3" format="tabular" from_work_dir="ORFs_max" label="${tool.name} on ${on_string}: Translated ORFs (max)"/>
+        <data name="output4" format="tabular" from_work_dir="ORFs_max_filt" label="${tool.name} on ${on_string}: Translated ORFs (max_filt)"/>
+        <data name="output5" format="bed" from_work_dir="translated_ORFs_sorted.bed" label="${tool.name} on ${on_string}: Translated ORFs (sorted)"/>
+        <data name="output6" format="bed" from_work_dir="translated_ORFs_filtered_sorted.bed" label="${tool.name} on ${on_string}: Translated ORFs (filtered/sorted)"/>
+        <data name="output7" format="fasta" from_work_dir="protein_db_max.fasta" label="${tool.name} on ${on_string}: Protein DB"/>
+        <data name="output8" format="pdf" from_work_dir="Final_ORF_results.pdf" label="${tool.name} on ${on_string}: ORF categories (length/coverage)"/>
     </outputs>
     <tests>
-        <test>
-            <param name="annotation_path" value="annotation_path.tgz" ftype="tar"/>
+        <test expect_num_outputs="8">
+            <param name="annotation_path" value="annotation_path.tgz"/>
             <param name="ribo_bam" value="test_ribo.bam"/>
             <param name="rna_bam" value="test_rna.bam"/>
             <output name="output2" file="ORFs_genes_found"/>
@@ -96,7 +109,5 @@
 PDF file containing info about the number of ORFs found, together with their length and coverage per category/annotation.
 
 ]]></help>
-    <citations>
-        <citation type="doi">10.1038/nmeth.3688</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>