# HG changeset patch
# User chrisw
# Date 1573707896 0
# Node ID 1ec6238425acb5af319b89c65088ae868044644c
# Parent  f158bf75c44c55c61c98055fa9d14ee0dfe4c44e
Uploaded

diff -r f158bf75c44c -r 1ec6238425ac monorail.xml
--- a/monorail.xml	Wed Nov 13 23:55:04 2019 +0000
+++ b/monorail.xml	Thu Nov 14 05:04:56 2019 +0000
@@ -70,7 +70,7 @@
 
  <!-- Genome source. -->
         <conditional name="refGenomeSource">
-                        <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome index set" help="If your genome of interest is not listed, contact the Galaxy team">
+                        <param name="genomeDir" type="select" label="Select reference genome index set" help="If your genome of interest is not listed, contact the Galaxy team">
                             <options from_data_table="monorail_index">
                                 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                             </options>
diff -r f158bf75c44c -r 1ec6238425ac tool-data/monorail_index.loc.sample
--- a/tool-data/monorail_index.loc.sample	Wed Nov 13 23:55:04 2019 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of rna-star indexed sequences data files. You will
-#need to create these data files and then create a rnastar_index2.loc
-#file similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The rnastar_index2.loc
-#file has this format (longer white space characters are TAB characters):
-#
-#<unique_build_id>   <dbkey>   <display_name>   <file_base_path> <withGTF>
-#
-#The <with_gtf> column should be 1 or 0, indicating whether the index was made
-#with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not,
-#respecively.
-#
-#Note that STAR indices can become quite large. Consequently, it is only
-#advisable to create indices with annotations if it's known ahead of time that
-#(A) the annotations won't be frequently updated and (B) the read lengths used
-#will also rarely vary. If either of these is not the case, it's advisable to
-#create indices without annotations and then specify an annotation file and
-#maximum read length (minus 1) when running STAR.
-#
-#hg19   hg19    hg19 full   /mnt/galaxyIndices/genomes/hg19/rnastar 0
-#hg19Ensembl   hg19Ensembl    hg19 full with Ensembl annotation   /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1
diff -r f158bf75c44c -r 1ec6238425ac tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed Nov 13 23:55:04 2019 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<tables>
-    <table name="monorail_index" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/monorail_index.loc" />
-    </table>
-</tables>