Mercurial > repos > trinity_ctat > ctat_fusion_inspector

changeset 2:b5be90bbe415 draft

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Updating fusion-inspector to work with the new datamanager (the tablename was changed to be consistent with other naming).
author trinity_ctat
date Wed, 16 May 2018 14:47:37 -0400
parents 2e98a907f573
children 1f894f083a45
files ctat_fusion_inspector.xml
diffstat 1 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/ctat_fusion_inspector.xml	Fri Apr 27 16:05:42 2018 -0400
+++ b/ctat_fusion_inspector.xml	Wed May 16 14:47:37 2018 -0400
@@ -7,7 +7,7 @@
       <![CDATA[
       FusionInspector 
       --fusions $fusion_candidates_list
-      --genome_lib "${genome_ref_lib.fields.path}"
+      --genome_lib "${genome_resource_lib.fields.path}"
       --left_fq $left_input
       --right $right_input
       --out_dir "subdir"
@@ -43,8 +43,8 @@
              <option value="false">False</option>
            </param>
       </conditional>
-      <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>
@@ -76,8 +76,8 @@
         <param name="method" value="STAR" />
         -->
         <param name="trinity" value="false" />
-        <!-- 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="?????" />
+        <!-- FIX - now that we added the CTAT resource lib path as a parameter, how do we find it for testing?
+        <param name="genome_resource_lib.fields.path" value="?????" />
         -->
         <output name="finspector_idx" file="FusionInspector/test.reads_1_2.fa.fai" />
         <output name="cytoBand" file="FusionInspector/test.reads_1_2.cytoBand.tail.txt" compare="contains" />