# HG changeset patch
# User jjohnson
# Date 1507209979 14400
# Node ID 5748e43a73e09ba242a2e9c29d4ee9a073c820ff
# Parent  5ff7593a7220b06e1f5a0bf048f2de9c1856a694
Uploaded

diff -r 5ff7593a7220 -r 5748e43a73e0 ._star_fusion.xml
Binary file ._star_fusion.xml has changed
diff -r 5ff7593a7220 -r 5748e43a73e0 star_fusion.xml
--- a/star_fusion.xml	Wed Oct 04 15:23:36 2017 -0400
+++ b/star_fusion.xml	Thu Oct 05 09:26:19 2017 -0400
@@ -6,6 +6,7 @@
     </requirements>
 
     <stdio>
+        <regex match="Can't locate " source="stderr" level="fatal"/>
         <regex match="command not found" source="stderr" level="fatal"/>
         <regex match="EXITING because of INPUT ERROR" source="stderr" level="fatal"/>
         <regex match="FATAL ERROR" source="stderr" level="fatal"/>
@@ -26,7 +27,7 @@
     <version_command>STAR-Fusion --version  2>&amp;1 | grep version | grep -o -E "software version.*?"</version_command>
 
     <command><![CDATA[
-        #if reference.reference_type_selector == 'cached':
+        #if $reference.reference_type_selector == 'cached':
             ln -s '$reference.ctat_resource_lib'  tmp_star_fusion_genome_dir
         #else
             ## 1. ensure the blastn file is provided as *.gz
@@ -82,8 +83,9 @@
             #end if
 
             --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir"
+            --output_dir "\$(pwd)"
 
-            str($input_params.optional_outputs).replace(',',' ')
+            #echo str($input_params.optional_outputs).replace(',',' ')
 
         #if str($params.settingsType) == "full":
             --min_junction_reads $params.min_junction_reads
@@ -100,11 +102,11 @@
     <inputs>
         <conditional name="reference">
             <param name="reference_type_selector" type="select" label="Star Fusion Genome Reference Source">
-                <option value="cached">Locally Cached sequences</option>
-                <option value="build" selected="true">Sequences from your history</option>
+                <option value="cached">Locally Cached Star Fusion Genome Reference</option>
+                <option value="build">Build a Star Fusion Genome Reference</option>
             </param>
             <when value="cached">
-                <param name="ctat_resource_lib" type="select" label="Genome to search">
+                <param name="ctat_resource_lib" type="select" label="Star Fusion Genome to search">
                     <options from_data_table="ctat_resource">
                         <column name="dbkey" index="1"/>
                         <column name="name" index="2"/>
@@ -162,7 +164,7 @@
                        format="interval"
                        argument="--chimeric_junction"
                        label="Chimeric junction file from STAR (with STAR-Fusion settings)"/>
-                 <param name="optional_outputs" type="select" multiple="true" label="Additional Outputs">
+                 <param name="optional_outputs" type="select" display="checkboxes" multiple="true" label="Additional Outputs">
                      <option value="--annotate">--annotate</option>
                      <option value="--examine_coding_effect">--examine_coding_effect</option>
                  </param>
@@ -179,7 +181,7 @@
                        optional="true"
                        argument="--right_fq"
                        label="right.fq file (actually optional, but highly recommended)"/>
-                 <param name="optional_outputs" type="select" multiple="true" label="Additional Outputs">
+                 <param name="optional_outputs" type="select" display="checkboxes" multiple="true" label="Additional Outputs">
                      <option value="--annotate">--annotate</option>
                      <option value="--examine_coding_effect">--examine_coding_effect</option>
                      <option value="--extract_fusion_reads">--extract_fusion_reads</option>