diff cuffcompare_wrapper.xml @ 2:8b22e9adae34

Update to the new data table specification.

--- a/cuffcompare_wrapper.xml	Tue Oct 01 15:12:23 2013 -0400
+++ b/cuffcompare_wrapper.xml	Wed Dec 04 13:24:29 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="cuffcompare" name="Cuffcompare" version="0.0.5">
+<tool id="cuffcompare" name="Cuffcompare" version="0.0.6">
     <!-- Wrapper supports Cuffcompare versions v1.3.0 and newer -->
     <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description>
     <requirements>
@@ -18,14 +18,12 @@
             
             ## Use sequence data?
             #if $seq_data.use_seq_data == "Yes":
-	        -s
+            -s
                 #if $seq_data.seq_source.index_source == "history":
                     --ref_file=$seq_data.seq_source.ref_file
                 #else:
-                    --ref_file="None"
+                    --index=${seq_data.seq_source.index.fields.path}
                 #end if
-                --dbkey=${first_input.metadata.dbkey} 
-                --index_dir=${GALAXY_DATA_INDEX_DIR}
             #end if
             
             ## Outputs.
@@ -67,7 +65,14 @@
                     <option value="cached">Locally cached</option>
                     <option value="history">History</option>
                   </param>
-                  <when value="cached"></when>
+                  <when value="cached">
+                    <param name="index" type="select" label="Using reference genome">
+                      <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="first_input" key="dbkey" column="1" />
+                        <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
+                      </options>
+                    </param>
+                  </when>
                   <when value="history">
                       <param name="ref_file" type="data" format="fasta" label="Using reference file" />
                   </when>