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changeset 26:0c16cad5e03b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
author iuc
date Sat, 03 Aug 2019 06:09:26 -0400
parents 3fb01a8c902d
children a86e80d3c09c
files hisat2.xml hisat2_macros.xml
diffstat 2 files changed, 133 insertions(+), 33 deletions(-) [+]
line wrap: on
line diff
--- a/hisat2.xml	Sat Jan 26 04:45:24 2019 -0500
+++ b/hisat2.xml	Sat Aug 03 06:09:26 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy4" profile="17.01">
+<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy5" profile="17.01">
     <description>A fast and sensitive alignment program</description>
     <macros>
         <import>hisat2_macros.xml</import>
@@ -575,44 +575,146 @@
 
         <!-- BAM -->
         <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM)">
-            <expand macro="dbKeyActions" />
+            <actions>
+                <expand macro="dbKeyActions" />
+            </actions>
         </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" />
+            <actions>
+                <conditional name="library.type">
+                    <when value="single">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="ext" />
+                        </action>
+                    </when>
+                    <when value="paired">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="ext" />
+                        </action>
+                    </when>
+                    <when value="paired_collection">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
+                        </action>
+                    </when>
+                    <when value="paired_interleaved">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
+                        </action>
+                    </when>
+                </conditional>
+                <expand macro="dbKeyActions" />
+            </actions>
         </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" />
+            <actions>
+                <conditional name="library.type">
+                    <when value="single">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="ext" />
+                        </action>
+                    </when>
+                    <when value="paired">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="ext" />
+                        </action>
+                    </when>
+                    <when value="paired_collection">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
+                        </action>
+                    </when>
+                    <when value="paired_interleaved">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
+                        </action>
+                    </when>
+                </conditional>
+                <expand macro="dbKeyActions" />
+            </actions>
         </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" />
+            <actions>
+                <conditional name="library.type">
+                    <when value="single">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="ext" />
+                        </action>
+                    </when>
+                    <when value="paired">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="ext" />
+                        </action>
+                    </when>
+                    <when value="paired_collection">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
+                        </action>
+                    </when>
+                    <when value="paired_interleaved">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
+                        </action>
+                    </when>
+                </conditional>
+                <expand macro="dbKeyActions" />
+            </actions>
         </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" />
+            <actions>
+                <conditional name="library.type">
+                    <when value="single">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="ext" />
+                        </action>
+                    </when>
+                    <when value="paired">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="ext" />
+                        </action>
+                    </when>
+                    <when value="paired_collection">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
+                        </action>
+                    </when>
+                    <when value="paired_interleaved">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
+                        </action>
+                    </when>
+                </conditional>
+                <expand macro="dbKeyActions" />
+            </actions>
         </data>
 
-        <!-- Alignment summary file -->
-        <data name="summary_file"  format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary" >
-          <filter>sum['summary_file'] is True</filter>
-          <expand macro="dbKeyActions" />
-        </data>
+     <!-- Alignment summary file -->
+    <data name="summary_file" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary">
+        <filter>sum['summary_file'] is True</filter>
+        <actions>
+            <expand macro="dbKeyActions" />
+        </actions>
+    </data>
 
-        <!-- Novel Splice file -->
-        <data name="novel_splicesite_output"  format="tabular" label="${tool.name} on ${on_string}: Novel Splice Sites" >
-          <filter>adv['spliced_options']['spliced_options_selector'] == 'advanced' and adv['spliced_options']['novel_splicesite_outfile'] is True</filter>
-          <expand macro="dbKeyActions" />
-        </data>
+    <!-- Novel Splice file -->
+    <data name="novel_splicesite_output" format="tabular" label="${tool.name} on ${on_string}: Novel Splice Sites">
+        <filter>adv['spliced_options']['spliced_options_selector'] == 'advanced' and adv['spliced_options']['novel_splicesite_outfile'] is True</filter>
+        <actions>
+            <expand macro="dbKeyActions" />
+        </actions>
+    </data>
 
 
     </outputs>
--- a/hisat2_macros.xml	Sat Jan 26 04:45:24 2019 -0500
+++ b/hisat2_macros.xml	Sat Aug 03 06:09:26 2019 -0400
@@ -29,22 +29,20 @@
     </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>
+        <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>
     </xml>
 
-</macros>
\ No newline at end of file
+</macros>