diff macros.xml @ 9:8c4c97fd0555 draft

"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"

--- a/macros.xml	Mon Oct 11 19:00:45 2021 +0000
+++ b/macros.xml	Wed Oct 13 18:45:16 2021 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.1.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
@@ -16,6 +16,36 @@
     <xml name="version_command">
         <version_command>arriba -h | grep Version | sed 's/^.* //'</version_command>
     </xml>
+    <xml name="genome_source" token_assembly_optional="false" >
+        <conditional name="genome">
+            <param name="genome_source" type="select" label="Arriba Genome assembly and annotation source">
+                <option value="history">From your history</option>
+                <option value="cached">Use built-in Arriba</option>
+            </param>
+            <when value="history">
+                <param name="assembly" argument="-a" type="data" format="fasta" optional="@ASSEMBLY_OPTIONAL@" label="Genome assembly fasta"/>
+                <param name="annotation" argument="-g" type="data" format="gtf" label="Gene annotation in GTF format"/>
+            </when>
+            <when value="cached">
+                <param name="arriba_ref" type="select" label="Arriba Genome assembly and annotation">
+                    <options from_data_table="arriba_indexes">
+                    </options>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@GENOME_SOURCE@">
+#if str($genome.genome_source) == "history"
+    #if $genome.assembly
+        #set $genome_assembly = $genome.assembly
+    #end if
+    #set $genome_annotation = $genome.annotation
+#else
+    #set $genome_assembly = $genome.arriba_ref.fields.fasta
+    #set $genome_annotation = $genome.arriba_ref.fields.gtf
+#end if
+</token>
+
     <xml name="visualization_options">
                 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
                 <section name="options" expanded="false" title="Draw Fusion Options">
@@ -127,7 +157,7 @@
 draw_fusions.R
     --fusions='$fusions'
     --alignments='Aligned.sortedByCoord.out.bam'
-    --annotation='$annotation'
+    --annotation='$genome.annotation'
     --output=fusions.pdf
     #if $visualization.cytobands
     --cytobands='$visualization.cytobands'