Mercurial > repos > trinity_ctat > ctat_star_fusion
changeset 4:31beded40e1a draft
Updating star_fusion and gmap_fusion to work with the new datamanager (the tablename was changed to be consistent with other naming).
| author | trinity_ctat |
|---|---|
| date | Wed, 16 May 2018 14:33:58 -0400 |
| parents | 853bfaeea21c |
| children | 42322c98b6ee |
| files | ctat_star_fusion.xml |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/ctat_star_fusion.xml Fri Apr 27 16:03:44 2018 -0400 +++ b/ctat_star_fusion.xml Wed May 16 14:33:58 2018 -0400 @@ -30,7 +30,7 @@ <command detect_errors="default"> <![CDATA[ STAR-Fusion - --genome_lib_dir "${genome_ref_lib.fields.path}" + --genome_lib_dir "${genome_resource_lib.fields.path}" --left_fq "${left_input}" --right_fq "${right_input}" --output_dir subdir @@ -40,8 +40,8 @@ <inputs> <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> - <param name="genome_ref_lib" type="select" label="Select a reference genome"> - <options from_data_table="ctat_genome_ref_libs"> + <param name="genome_resource_lib" type="select" label="Select a reference genome"> + <options from_data_table="ctat_genome_resource_libs"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> @@ -63,7 +63,7 @@ <param name="right_input" value="reads.right.simPE.fq" /> --> <!-- FIX - now that we added the CTAT ref lib path as a parameter, how do we find it for testing? - <param name="genome_ref_lib.fields.path" value="?????" /> + <param name="genome_resource_lib.fields.path" value="?????" /> --> <!-- <output name="aligned_bam" file="SF_out_aligned.bam" />