diff macros.xml @ 0:f7c0a0030254 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue May 23 13:43:07 2023 +0000
@@ -0,0 +1,63 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.1.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">agat</requirement>
+            <requirement type="package" version="0.34">perl-statistics-r</requirement>
+        </requirements>
+    </xml>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">agat</xref>
+        </xrefs>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.5281/zenodo.3552717</citation>
+        </citations>
+    </xml>
+    <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="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.">
+                <option value="indexed" selected="true">Use a built-in genome</option>
+                <option value="history" selected="true">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>
+    </xml>
+    <token name="@input_annotation_single@"><![CDATA[
+        #set $input_annotation = 'annotation.' + str($tool.gff.ext)
+        ln -s '${tool.gff}' $input_annotation &&
+    ]]></token>
+    <token name="@input_reference@"><![CDATA[
+        #if $tool.reference_genome.source == 'history':
+            #set $ref_genome = 'reference.fasta'
+            ln -s -f '${tool.reference_genome.history_item}' $ref_genome &&
+        #else:
+            #set $ref_genome = $tool.reference_genome.index.fields.path
+        #end if
+    ]]></token>
+    <token name="@input_annotation_double@"><![CDATA[
+        #set $input1 = 'annotation1.' + str($tool.input_annotation1.ext)
+        #set $input2 = 'annotation2.' + str($tool.input_annotation2.ext)
+        ln -s '${tool.input_annotation1}' $input1 &&
+        ln -s '${tool.input_annotation2}' $input2 &&
+    ]]></token>
+    
+
+</macros>