# HG changeset patch
# User iuc
# Date 1528569219 14400
# Node ID d5659efd66aaefb24fe0ef2b5d9ca83e03adbece
# Parent  a70a7eebb4350d87cbbfdf9b10c977de16daf677
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167

diff -r a70a7eebb435 -r d5659efd66aa macros.xml
--- a/macros.xml	Wed May 16 17:31:03 2018 -0400
+++ b/macros.xml	Sat Jun 09 14:33:39 2018 -0400
@@ -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>
diff -r a70a7eebb435 -r d5659efd66aa rg_rnaStar.xml
--- a/rg_rnaStar.xml	Wed May 16 17:31:03 2018 -0400
+++ b/rg_rnaStar.xml	Sat Jun 09 14:33:39 2018 -0400
@@ -384,91 +384,30 @@
     </inputs>
 
     <outputs>
-        <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
+        <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out">
+            <expand macro="dbKeyActions" />
+        </data>
         <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction">
             <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )</filter>
-            <actions>
-                <conditional name="refGenomeSource.geneSource">
-                    <when value="indexed">
-                        <action type="metadata" name="dbkey">
-                            <option type="from_data_table" name="rnastar_index" 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>
+            <expand macro="dbKeyActions" />
         </data>
 
         <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam">
             <filter>params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0</filter>
-            <actions>
-                <conditional name="refGenomeSource.geneSource">
-                    <when value="indexed">
-                        <action type="metadata" name="dbkey">
-                            <option type="from_data_table" name="rnastar_index" 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>
+            <expand macro="dbKeyActions" />
         </data>
 
         <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab">
-            <actions>
-                <conditional name="refGenomeSource.geneSource">
-                    <when value="indexed">
-                        <action type="metadata" name="dbkey">
-                            <option type="from_data_table" name="rnastar_index" 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>
+            <expand macro="dbKeyActions" />
         </data>
 
         <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
-            <actions>
-                <conditional name="refGenomeSource.geneSource">
-                    <when value="indexed">
-                        <action type="metadata" name="dbkey">
-                            <option type="from_data_table" name="rnastar_index" 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>
+            <expand macro="dbKeyActions" />
         </data>
         
         <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
             <filter>quantMode is True</filter>
+            <expand macro="dbKeyActions" />
         </data>
     </outputs>