diff data_manager/macros.xml @ 4:6ef6520f14fc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2

--- a/data_manager/macros.xml	Mon Jan 15 15:39:25 2018 -0500
+++ b/data_manager/macros.xml	Wed Jul 18 13:26:12 2018 -0400
@@ -1,8 +1,8 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.5.2b">star</requirement>
-            <requirement type="package" version="0.1.19">samtools</requirement>
+            <requirement type="package" version="2.6.0b">star</requirement>
+            <requirement type="package" version="1.8">samtools</requirement>
         </requirements>
     </xml>
     <token name="@FASTQ_GZ_OPTION@">
@@ -17,4 +17,23 @@
          <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="true" help="Exon junction information for mapping splices"/>
          <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
     </xml>
+    <xml name="dbKeyActions">
+        <actions>
+            <conditional name="refGenomeSource.geneSource">
+                <when value="indexed">
+                    <action type="metadata" name="dbkey">
+                        <option type="from_data_table" name="rnastar_index2" column="1" offset="0">
+                            <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                            <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
+                        </option>
+                    </action>
+                </when>
+                <when value="history">
+                    <action type="metadata" name="dbkey">
+                        <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </xml>
 </macros>