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diff cuffdiff_wrapper.xml @ 3:beab768feb92

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Update to the new data table specification.
author Dave Bouvier <dave@bx.psu.edu>
date Wed, 04 Dec 2013 13:24:38 -0500
parents 2d6a90609943
children 604fa75232a2
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line diff
--- a/cuffdiff_wrapper.xml	Tue Oct 22 11:03:02 2013 -0400
+++ b/cuffdiff_wrapper.xml	Wed Dec 04 13:24:38 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="cuffdiff" name="Cuffdiff" version="0.0.6">
+<tool id="cuffdiff" name="Cuffdiff" version="0.0.7">
     <!-- Wrapper supports Cuffdiff versions 2.1.0-2.1.1 -->
     <description>find significant changes in transcript expression, splicing, and promoter use</description>
     <requirements>
@@ -33,7 +33,7 @@
                     $bias_correction.seq_source.ref_file
                 #else:
                     ## Built-in genome.
-                    ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
+                    ${__get_data_table_entry__('fasta_indexes', 'value', $gtf_input.dbkey, 'path')}
                 #end if
             #end if
 
@@ -89,7 +89,14 @@
                     <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="gtf_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>