changeset 3:b1e25f9b5eab draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059

--- a/hisat2.xml	Fri Jan 15 03:33:11 2016 -0500
+++ b/hisat2.xml	Tue Mar 15 13:04:50 2016 -0400
@@ -6,10 +6,13 @@
     </macros>
     <requirements>
         <requirement type="package" version="2.0">hisat</requirement>
+        <!-- Conda dependency -->
+        <requirement type="package" version="2.0.0beta">hisat2</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
     </requirements>
     <stdio>
         <regex match="hisat2-align exited with value 1" source="both" level="fatal"/>
+        <regex match="hisat2: not found" source="both" level="fatal"/>
         <exit_code range="1:" />
     </stdio>
     <version_command>hisat2 --version</version_command>
@@ -28,7 +31,7 @@
         #end if
         hisat2 -p \${GALAXY_SLOTS:-1} -x "${index_path}"
         #if str($input_format.paired.paired_selector) == 'paired':
-            -1 "${reads_f}" -2 "${reads_r}"
+            -1 "${input_format.paired.reads_f}" -2 "${input_format.paired.reads_r}"
             @paired_end_options@
         #else if str($input_format.paired.paired_selector) == 'paired_collection':
             -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}"
@@ -80,7 +83,7 @@
             --minins ${paired_options.minins} --maxins ${paired_options.maxins} ${paired_options.no_mixed} ${paired_options.no_discordant}
             ${paired_options.dovetail} ${paired_options.contain} ${paired_options.overlap}
         #end if
-        | samtools view -bS - | samtools sort - -o hsbam > "${output_alignments}"
+        | samtools sort - -@ \${GALAXY_SLOTS:-2} -l 6 -o hsbam > "${output_alignments}"
         ]]>
     </command>
     <inputs>
@@ -221,7 +224,25 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="bam" name="output_alignments" />
+        <data format="bam" name="output_alignments">
+            <actions>
+              <conditional name="reference_genome.reference_genome_source">
+                <when value="indexed">
+                  <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="hisat2_indexes" column="1" offset="0">
+                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                      <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>
+        </data>
     </outputs>
     <tests>
         <test>