# HG changeset patch
# User devteam
# Date 1483271492 18000
# Node ID 0849fa93eadbe2db31105ba95c965c5c0fa4d91e
# Parent  758594ed0364ac59320f20954fee352f315cd469
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d

diff -r 758594ed0364 -r 0849fa93eadb tophat2_wrapper.xml
--- a/tophat2_wrapper.xml	Mon May 09 10:33:50 2016 -0400
+++ b/tophat2_wrapper.xml	Sun Jan 01 06:51:32 2017 -0500
@@ -95,7 +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":
diff -r 758594ed0364 -r 0849fa93eadb tophat_macros.xml
--- a/tophat_macros.xml	Mon May 09 10:33:50 2016 -0400
+++ b/tophat_macros.xml	Sun Jan 01 06:51:32 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" />