changeset 4:c53938d8a6da draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 38b164ccb9b3cdfb58d83cdc1f05063a40123bab-dirty

--- a/all_fasta.loc.sample	Wed Aug 24 07:18:07 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-#This file lists the locations and dbkeys of all the fasta files
-#under the "genome" directory (a directory that contains a directory
-#for each build). The script extract_fasta.py will generate the file
-#all_fasta.loc. This file has the format (white space characters are
-#TAB characters):
-#
-#<unique_build_id>	<dbkey>	<display_name>	<file_path>
-#
-#So, all_fasta.loc could look something like this:
-#
-#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
-#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
-#
-#Your all_fasta.loc file should contain an entry for each individual
-#fasta file. So there will be multiple fasta files for each build,
-#such as with hg19 above.
-#

--- a/star_fusion.xml	Wed Aug 24 07:18:07 2016 -0400
+++ b/star_fusion.xml	Fri Aug 26 04:45:35 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-1" profile="16.07">
+<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-2" profile="16.07">
     <description>detect fusion genes in RNA-Seq data</description>
     <requirements>
         <!-- Bio-conda -->
@@ -6,6 +6,10 @@
     </requirements>
 
     <stdio>
+        <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"/>
+        
         <regex match="Warning:" source="stderr" level="warning"/>
         <regex match="CMD:" source="stderr" level="warning"/>
         
@@ -106,7 +110,10 @@
             <when value="cached">
                 <param name="ownFile"
                        type="select" label="Genome to search">
-                    <options from_data_table="all_fasta" />
+                    <options from_data_table="all_fasta">
+                        <column name="value" index="3"/>
+                        <column name="dbkey" index="1"/>
+                    </options>
                 </param>
             </when>
             <when value="history">

--- a/tool_data_table_conf.xml.sample	Wed Aug 24 07:18:07 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<tables>
-    <!-- Locations of all fasta files under genome directory -->
-    <table name="all_fasta" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/all_fasta.loc" />
-    </table>
-</tables>