Mercurial > repos > trinity_ctat > ctat_star_fusion

changeset 4:31beded40e1a draft

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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(-) [+]
line wrap: on
line diff
--- 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" />