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changeset 20:6ab42baa56e9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d9ebd463afa1a41799aa53e9a68d0ea51093007e
author iuc
date Wed, 30 May 2018 12:02:20 -0400
parents fbf98f24097b
children 0b1c04a90182
files hisat2.xml hisat2_macros.xml
diffstat 2 files changed, 28 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/hisat2.xml	Tue Apr 10 18:41:43 2018 -0400
+++ b/hisat2.xml	Wed May 30 12:02:20 2018 -0400
@@ -536,31 +536,38 @@
     <outputs>
 
         <!-- BAM -->
-        <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM) " />
+        <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM)">
+            <expand macro="dbKeyActions" />
+        </data>
 
         <!-- Unaligned fastq (L) -->
         <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)">
             <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True</filter>
+            <expand macro="dbKeyActions" />
         </data>
 
         <!-- Aligned fastq (L) -->
         <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (L)">
             <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True</filter>
+            <expand macro="dbKeyActions" />
         </data>
 
         <!-- Unaligned fastq (R) -->
         <data name="output_unaligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (R)">
             <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True) </filter>
+            <expand macro="dbKeyActions" />
         </data>
 
         <!-- Aligned fastq (R) -->
         <data name="output_aligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (R)">
             <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True) </filter>
+            <expand macro="dbKeyActions" />
         </data>
 
         <!-- Alignment summary file -->
         <data name="summary_file"  format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary" >
           <filter>sum['summary_file'] is True</filter>
+          <expand macro="dbKeyActions" />
         </data>
 
     </outputs>
--- a/hisat2_macros.xml	Tue Apr 10 18:41:43 2018 -0400
+++ b/hisat2_macros.xml	Wed May 30 12:02:20 2018 -0400
@@ -27,4 +27,24 @@
         </conditional>
 
     </xml>
+
+    <xml name="dbKeyActions">
+        <actions>
+            <conditional name="reference_genome.source">
+                <when value="indexed">
+                    <action type="metadata" name="dbkey">
+                         <option type="from_data_table" name="hisat2_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.history_item" param_attribute="dbkey" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </xml>
+
 </macros>
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