changeset 23:17062a0decb7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7

--- a/bowtie2_macros.xml	Thu Apr 12 17:42:40 2018 -0400
+++ b/bowtie2_macros.xml	Wed Jun 06 17:23:32 2018 -0400
@@ -323,4 +323,20 @@
         <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc (possibly with -gz or -bz2); This triggers --un parameter for single reads and --un-conc for paired reads" />
         <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc (possibly with -gz or -bz2); This triggers --al parameter for single reads and --al-conc for paired reads" />
     </xml>
+    <xml name="dbKeyActions">
+        <conditional name="reference_genome.source">
+            <when value="indexed">
+                <action type="metadata" name="dbkey">
+                     <option type="from_data_table" name="bowtie2_indexes" column="1">
+                        <filter type="param_value" ref="reference_genome.index" column="0"/>
+                    </option>
+                </action>
+            </when>
+            <when value="history">
+                <action type="metadata" name="dbkey">
+                    <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
+                </action>
+            </when>
+        </conditional>
+    </xml>
 </macros>

--- a/bowtie2_wrapper.xml	Thu Apr 12 17:42:40 2018 -0400
+++ b/bowtie2_wrapper.xml	Wed Jun 06 17:23:32 2018 -0400
@@ -557,6 +557,7 @@
                         </action>
                     </when>
                 </conditional>
+                <expand macro="dbKeyActions" />
             </actions>
         </data>
         <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
@@ -579,6 +580,7 @@
                         </action>
                     </when>
                 </conditional>
+                <expand macro="dbKeyActions" />
             </actions>
         </data>
         <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
@@ -596,6 +598,7 @@
                         </action>
                     </when>
                 </conditional>
+                <expand macro="dbKeyActions" />
             </actions>
         </data>
         <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
@@ -613,6 +616,7 @@
                         </action>
                     </when>
                 </conditional>
+                <expand macro="dbKeyActions" />
             </actions>
         </data>
         <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (BAM)">
@@ -636,6 +640,7 @@
                 </action>
               </when>
             </conditional>
+            <expand macro="dbKeyActions" />
           </actions>
         </data>
         <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
@@ -656,10 +661,14 @@
                 </action>
               </when>
             </conditional>
+            <expand macro="dbKeyActions" />
           </actions>
         </data>
         <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
           <filter>save_mapping_stats is True</filter>
+          <actions>
+            <expand macro="dbKeyActions" />
+          </actions>
         </data>
     </outputs>
     <tests>