# HG changeset patch
# User devteam
# Date 1483271479 18000
# Node ID d1009ebd6f15b4466654d4ebcba60282a4dfacc2
# Parent  1449cb926fcec93b5cb9fd2f214e4f2cccef77d4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d

diff -r 1449cb926fce -r d1009ebd6f15 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Dec 18 19:17:38 2015 -0500
+++ b/tool_dependencies.xml	Sun Jan 01 06:51:19 2017 -0500
@@ -3,7 +3,7 @@
   <package name="bowtie2" version="2.2.5">
       <repository changeset_revision="f5582ac5ba3c" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="tophat" version="2.0.14">
-      <repository changeset_revision="6887732aeab7" name="package_tophat_2_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="tophat" version="2.1.0">
+      <repository changeset_revision="121ea973aad8" name="package_tophat_2_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
diff -r 1449cb926fce -r d1009ebd6f15 tophat2_wrapper.xml
--- a/tophat2_wrapper.xml	Fri Dec 18 19:17:38 2015 -0500
+++ b/tophat2_wrapper.xml	Sun Jan 01 06:51:19 2017 -0500
@@ -1,11 +1,46 @@
-<tool id="tophat2" name="TopHat" version="0.9">
+<tool id="tophat2" name="TopHat" version="2.1.0">
     <!-- Wrapper compatible with Tophat version 2.0.0+ -->
     <description>Gapped-read mapper for RNA-seq data</description>
-    <version_command>tophat2 --version</version_command>
+    <macros>
+      <import>tophat_macros.xml</import>
+      <xml name="paired_parameters">
+        <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" help="-r/--mate-inner-dist; This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 50bp."/>
+        <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs"  help="--mate-std-dev; The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp."/>
+        <!-- Discordant pairs. -->
+        <param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?" help="--no-discordant">
+            <option value="No">No</option>
+            <option selected="True" value="Yes">Yes</option>
+        </param>
+      </xml>
+      <macro name="dbKeyActions">
+        <actions>
+          <conditional name="refGenomeSource.genomeSource">
+            <when value="indexed">
+              <action type="metadata" name="dbkey">
+                <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
+                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                  <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                </option>
+              </action>
+            </when>
+            <when value="history">
+              <action type="metadata" name="dbkey">
+                <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+              </action>
+            </when>
+          </conditional>
+        </actions>
+      </macro>
+    </macros>
     <requirements>
         <requirement type="package" version="2.2.5">bowtie2</requirement>
-        <requirement type="package" version="2.0.14">tophat</requirement>
+        <requirement type="package" version="2.1.0">tophat</requirement>
     </requirements>
+    <stdio>
+        <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/>
+        <regex match=".*" source="both" level="log" description="tool progress"/>
+    </stdio>
+    <version_command>tophat2 --version</version_command>
 
     <command>
         ##
@@ -60,7 +95,9 @@
 
             ## Supplying junctions parameters.
             #if $params.own_junctions.use_junctions == "Yes":
-                #if $params.own_junctions.gene_model_ann.use_annotations == "Yes":
+                #if $params.own_junctions.gene_model_ann.use_annotations == "indexed"
+                    -G $params.own_junctions.gene_model_ann.gene_annotation_model.fields.path
+                #elif $params.own_junctions.gene_model_ann.use_annotations == "history"
                     -G $params.own_junctions.gene_model_ann.gene_annotation_model
                 #end if
                 #if $params.own_junctions.raw_juncs.use_juncs == "Yes":
@@ -75,7 +112,7 @@
                 --coverage-search
                 --min-coverage-intron $params.coverage_search.min_coverage_intron
                 --max-coverage-intron $params.coverage_search.max_coverage_intron
-            #else:
+            #elif $params.coverage_search.use_search == "No"
                 --no-coverage-search
             #end if
 
@@ -193,10 +230,12 @@
               <expand macro="own_junctionsConditional" />
               <!-- Coverage search. -->
               <conditional name="coverage_search">
-                <param name="use_search" type="select" label="Use Coverage Search" help="Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.">
-                    <option selected="true" value="No">No</option>
-                    <option value="Yes">Yes</option>
+                <param name="use_search" type="select" label="Use coverage-based search for junctions" help="Select 'Auto' to let TopHat decide when to enable coverage search (e.g. disable it for reads 75bp or longer). Select 'Yes' to enforce maximum sensitivity and to specify minimum and maximum intron length">
+                    <option selected="true" value="auto">Auto</option>
+                    <option value="No">No (--no-coverage-search)</option>
+                    <option value="Yes">Yes (--coverage-search)</option>
                 </param>
+                <when value="auto" />
                 <when value="Yes">
                     <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" help="--min-coverage-intron; The minimum intron length that may be found during coverage search. The default is 50."/>
                     <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" help="--max-coverage-intron; The maximum intron length that may be found during coverage search. The default is 20000."/>
@@ -270,11 +309,6 @@
       </conditional> <!-- readGroup -->
     </inputs>
 
-    <stdio>
-        <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/>
-        <regex match=".*" source="both" level="log" description="tool progress"/>
-    </stdio>
-
     <outputs>
         <data format="txt" name="align_summary" label="${tool.name} on ${on_string}: align_summary" from_work_dir="tophat_out/align_summary.txt"/>
         <data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out">
@@ -299,38 +333,6 @@
 
     </outputs>
 
-    <macros>
-      <import>tophat_macros.xml</import>
-      <xml name="paired_parameters">
-        <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" help="-r/--mate-inner-dist; This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 50bp."/>
-        <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs"  help="--mate-std-dev; The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp."/>
-        <!-- Discordant pairs. -->
-        <param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?" help="--no-discordant">
-            <option value="No">No</option>
-            <option selected="True" value="Yes">Yes</option>
-        </param>
-      </xml>
-      <macro name="dbKeyActions">
-        <actions>
-          <conditional name="refGenomeSource.genomeSource">
-            <when value="indexed">
-              <action type="metadata" name="dbkey">
-                <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
-                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                  <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                </option>
-              </action>
-            </when>
-            <when value="history">
-              <action type="metadata" name="dbkey">
-                <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-              </action>
-            </when>
-          </conditional>
-        </actions>
-      </macro>
-    </macros>
-
     <tests>
         <!-- Test base-space single-end reads with pre-built index and preset parameters -->
         <test>
diff -r 1449cb926fce -r d1009ebd6f15 tophat_macros.xml
--- a/tophat_macros.xml	Fri Dec 18 19:17:38 2015 -0500
+++ b/tophat_macros.xml	Sun Jan 01 06:51:19 2017 -0500
@@ -36,14 +36,20 @@
       </param>
       <when value="Yes">
         <conditional name="gene_model_ann">
-          <param name="use_annotations" type="select" label="Use Gene Annotation Model">
+          <param name="use_annotations" type="select" label="Use Gene Annotation Model" help="-G/--GTF; TopHat with a set of gene model annotations and/or known transcripts, as a GTF 2.2 or GFF3 formatted file. If this option is provided, TopHat will first extract the transcript sequences and use Bowtie to align reads to this virtual transcriptome first. Only the reads that do not fully map to the transcriptome will then be mapped on the genome. The reads that did map on the transcriptome will be converted to genomic mappings (spliced as needed) and merged with the novel mappings and junctions in the final tophat output. Please note that the values in the first column of the provided GTF/GFF file (column which indicates the chromosome or contig on which the feature is located), must match the name of the reference sequence in the Bowtie index you are using with TopHat.">
             <option value="No">No</option>
-            <option value="Yes">Yes</option>
+             <option value="indexed">Use a built-in gene annotation</option>
+            <option value="history">Use a gene annotation from history</option>
           </param>
           <when value="No" />
-          <when value="Yes">
-            <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="-G/--GTF; TopHat with a set of gene model annotations and/or known transcripts, as a GTF 2.2 or GFF3 formatted file. If this option is provided, TopHat will first extract the transcript sequences and use Bowtie to align reads to this virtual transcriptome first. Only the reads that do not fully map to the transcriptome will then be mapped on the genome. The reads that did map on the transcriptome will be converted to genomic mappings (spliced as needed) and merged with the novel mappings and junctions in the final tophat output. Please note that the values in the first column of the provided GTF/GFF file (column which indicates the chromosome or contig on which the feature is located), must match the name of the reference sequence in the Bowtie index you are using with TopHat."/>
+          <when value="indexed">
+            <param format="gtf,gff3" name="gene_annotation_model" type="select" label="Gene Model Annotations">
+                <options from_data_table="gff_gene_annotations"/>
+             </param>
           </when>
+          <when value="history">
+            <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" metadata_name="dbkey" />
+          </when>  
         </conditional>
         <expand macro="raw_juncsConditional" />
         <expand macro="no_novel_juncsParam" />