--- a/ribotaper_part1_create_annotation_files.xml	Wed Nov 30 16:57:07 2016 -0500
+++ b/ribotaper_part1_create_annotation_files.xml	Fri Jun 03 20:17:28 2022 +0000
@@ -1,46 +1,68 @@
-<tool id="ribotaper_create_annotation" name="ribotaper part 1: creation of annotation files" version="0.1.0">
-    <requirements>
-            <requirement type="package" version="1.3.1a">ribotaper</requirement>
-    </requirements>
+<tool id="ribotaper_create_annotation" name="ribotaper part 1: creation of annotation files" 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:" />
+        <exit_code range="1:"/>
     </stdio>
-
     <command><![CDATA[
-        create_annotations_files.bash
-            "$gtf"
-            "$fa"
-            "$ccdsid"
-            "$appris"
-            "annotation_path"
+        #if $reference_genome.source == 'history':
+            #set $ref_genome = 'reference.fasta'
+            ln -s -f '${reference_genome.history_item}' $ref_genome
+            && samtools faidx $ref_genome
+        #else:
+            #set $ref_genome = $reference_genome.index.fields.path
+        #end if
+        && create_annotations_files.bash
+        '${gtf}'
+        '${ref_genome}'
+        $ccdsid
+        $appris
+        './annotation_path'
         &&
-        tar
-            "czvf"
-            "$output2"
-            "annotation_path"
+        tar czvf '${output2}' './annotation_path'
 
     ]]></command>
     <inputs>
-        <param name="gtf" type="data" format="GTF" label="GTF"
-               help="GTF should contain:
-               1) coding and non-coding genes, 2) a 'transcript_id' and a 'gene_id' field for each 'exon' and 'CDS' row.
-               "/>
-        <param name="fa" type="data" format="fasta" label="Genome fasta file" help="FASTA-format, indexed and not repeat masked."/>
-        <param name="ccdsid" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use ccdsid? (valid for Human Gencode 19 and Mouse Gencode M3 )"
-               help="If yes, only exons/transcripts with the CCDS tag will be used as CCDS exons/transcripts, otherwise all exons/transcripts with a CDS region are going to be annotated as CCDS.
-                    "/>
-        <param name="appris" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use appris? (valid for Human Gencode 19 and Mouse Gencode M3 )"
-               help=" If yes, only exons/transcripts with the appris tag will be used, using only 1 transcript per appris gene (the appris_principal transcript or other appris transcript). If a               gene does not have appris transcript, all the annotated transcript structures are used.
-               "/>
+        <param name="gtf" type="data" format="GTF" label="Annotation file"
+            help="The GTF file should contain: 1) coding and non-coding genes, 2) a 'transcript_id' and a 'gene_id' field for each 'exon' and 'CDS' row."/>
+        <conditional name="reference_genome">
+            <param name="source" type="select" label="Source for the genome" help="Built-in references were created using default options.">
+                <option value="indexed" selected="true">Use a built-in genome</option>
+                <option value="history">Use a genome from history</option>
+            </param>
+            <when value="indexed">
+                <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team.">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="sort_by" column="2" />
+                        <validator type="no_options" message="No genomes are available for the selected input dataset" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
+            </when>
+        </conditional>
+        <param name="ccdsid" type="boolean" falsevalue="false" truevalue="true" checked="true" 
+            label="Use CCDS annotation (valid for Human Gencode 19 and Mouse Gencode M3)"
+            help="If yes, only exons/transcripts with the CCDS tag will be used as CCDS exons/transcripts, otherwise all exons/transcripts with a CDS region are going to be annotated as CCDS."/>
+        <param name="appris" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use Appris annotation (valid for Human Gencode 19 and Mouse Gencode M3)"
+               help=" If yes, only exons/transcripts with the appris tag will be used, using only 1 transcript per appris gene (the appris_principal transcript or other appris transcript). 
+                If a gene does not have appris transcript, all the annotated transcript structures are used."/>
     </inputs>
     <outputs>
-        <data name="output1" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/>
-        <data name="output2" format="tar" label="annotation_path"/>
+        <data name="output1" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="${tool.name} on ${on_string}: start_stops FAR"/>
+        <data name="output2" format="tgz" label="${tool.name} on ${on_string}: Annotation path"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="gtf" value="test.gtf"/>
-            <param name="fa" value="test.fa"/>
+            <conditional name="reference_genome">
+                <param name="source" value="history"/>
+                <param name="history_item" value="test.fa"/>
+            </conditional>
             <param name="ccdsid" value="true"/>
             <param name="appris" value="true"/>
             <output name="output1" file="annotation_path/start_stops_FAR.bed"/>
@@ -88,7 +110,5 @@
 
 
 ]]></help>
-    <citations>
-        <citation type="doi">10.1038/nmeth.3688</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>