changeset 2:a10082746830 draft

Updating star_fusion and gmap_fusion to work with the new datamanager (the tablename was changed to be consistent with other naming).

--- a/ctat_gmap_fusion.xml	Fri Apr 27 16:07:05 2018 -0400
+++ b/ctat_gmap_fusion.xml	Wed May 16 14:37:32 2018 -0400
@@ -8,7 +8,7 @@
       -T $assembled_trans 
       --left_fq $left_input
       --right_fq $right_input
-      --genome_lib_dir "${genome_ref_lib.fields.path}"
+      --genome_lib_dir "${genome_resource_lib.fields.path}"
       --output "subdir" 
     </command>
     <stdio>
@@ -22,8 +22,8 @@
       <param format="fasta" name="assembled_trans" type="data" label="Assembled Transcripts (ie. Trinity or DISCASM output)" help="Trinity or DISCASM generated transcript fasta"/>
       <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help="Forward strand reads"/>
       <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help="Reverse strand reads"/>
-      <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>
@@ -39,7 +39,7 @@
         <param name="right_input" value="GMAP/reads_2.fq.gz" />
         <param name="assembled_trans" value="GMAP/transcripts.fa" />
         <!-- 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="gmapfusion_candidates" file="GMAP/fusion.reads_1_2.final" />
       </test>