Mercurial > repos > devteam > cuffmerge
diff cuffmerge_wrapper.xml @ 2:5b285b6e4ee3
Update to the new data table specification.
author | Dave Bouvier <dave@bx.psu.edu> |
---|---|
date | Wed, 04 Dec 2013 13:24:59 -0500 |
parents | dbbd37e013aa |
children | 68eaaae05c51 |
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--- a/cuffmerge_wrapper.xml Tue Oct 01 15:13:24 2013 -0400 +++ b/cuffmerge_wrapper.xml Wed Dec 04 13:24:59 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="cuffmerge" name="Cuffmerge" version="0.0.5"> +<tool id="cuffmerge" name="Cuffmerge" version="0.0.6"> <!-- Wrapper supports Cuffmerge versions 1.3 and newer --> <description>merge together several Cufflinks assemblies</description> <requirements> @@ -20,10 +20,8 @@ #if $seq_data.seq_source.index_source == "history": --ref_file=$seq_data.seq_source.ref_file #else: - --ref_file="None" + --index=${bias_correction.seq_source.index.fields.path} #end if - --dbkey=${first_input.metadata.dbkey} - --index_dir=${GALAXY_DATA_INDEX_DIR} #end if ## Outputs. @@ -64,7 +62,14 @@ <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="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>