diff macros.xml @ 2:e009d8260be2 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae

--- a/macros.xml	Tue May 23 18:05:26 2023 +0000
+++ b/macros.xml	Thu Sep 07 05:29:24 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.1.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">1.2.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">agat</requirement>
@@ -19,7 +19,36 @@
     <xml name="ANNOTATION_INPUT" token_format="gff,gtf,gff3,gff3.gz">
         <param argument="--gff" type="data" format="@FORMAT@" label="Annotation file" help="Input GTF/GFF file" />
     </xml>
-
+    <xml name="AGAT_CONFIG">
+        <conditional name="output_format">
+            <param name="selector" type="select" label="Output format">
+                <option value="GFF">GFF</option>
+                <option value="GTF">GTF</option>
+            </param>
+            <when value="GFF">
+                <param name="version" type="select" label="Format version">
+                    <option value="1">1</option>
+                    <option value="2">2</option>
+                    <option value="2.5">2.5</option>
+                    <option value="3" selected="true">3</option>
+                </param>
+            </when>
+            <when value="GTF">
+                <param name="version" type="select" label="Format version">
+                    <option value="1">1 = ("CDS", "start_codon", "stop_codon", "exon", "intron")</option>
+                    <option value="2">2 = ("CDS", "start_codon", "stop_codon", "exon")</option>
+                    <option value="2.1">2.1 = ("CDS", "start_codon", "stop_codon", "exon", "5UTR", "3UTR")</option>
+                    <option value="2.2">2.2 = ("CDS", "start_codon", "stop_codon", "5UTR", "3UTR", "inter", "inter_CNS", "intron_CNS", "exon")</option>
+                    <option value="2.5">2.5 = ("gene", "transcript", "exon", "CDS", "UTR", "start_codon", "stop_codon", "Selenocysteine")</option>
+                    <option value="3">3 = ("gene", "transcript", "exon", "CDS", "Selenocysteine", "start_codon", "stop_codon", "three_prime_utr", "five_prime_utr")</option>
+                    <option value="relax" selected="true">Relax = All feature types will be accepted</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="merge_loci" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge loci" help="Should overlapping loci (at CDS level) be merged in a single locus. Only one gene is kept, and the mRNA features become isoforms." />
+        <param name="create_exon" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Create exon when l2 do not have children"/>
+    </xml>
+    
     <xml name="REFERENCE_FASTA">
         <conditional name="reference_genome">
             <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">