# HG changeset patch
# User sanbi-uwc
# Date 1485950852 18000
# Node ID 4b9ddf64558df408a7a91f8deb2a62c10353d8c1
# Parent  cc255feec53b8736d0e2d9e838b7604199cc3158
planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit c467fa511c437e11ea72b912975d64631b8d0f98

diff -r cc255feec53b -r 4b9ddf64558d tool-data/all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Wed Feb 01 07:07:32 2017 -0500
@@ -0,0 +1,7 @@
+#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>
diff -r cc255feec53b -r 4b9ddf64558d tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Feb 01 07:07:32 2017 -0500
@@ -0,0 +1,6 @@
+<tables>
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>
diff -r cc255feec53b -r 4b9ddf64558d vcf_to_alignment.xml
--- a/vcf_to_alignment.xml	Wed Feb 01 06:56:24 2017 -0500
+++ b/vcf_to_alignment.xml	Wed Feb 01 07:07:32 2017 -0500
@@ -18,7 +18,7 @@
     #if str($reference.source) == 'history':
       reference.fasta
     #else
-      '${reference.builtin}'
+      '${reference.builtin.fields.path}'
     #end if
     --output_file '${output_alignment}'
     ]]>
@@ -36,6 +36,7 @@
       <when value="builtin">
         <param name="builtin" type="select" label="Reference sequence (FASTA format)">
           <options from_data_table="all_fasta" />
+          <validator type="no_options" message="No FASTA datasets are available for the selected input dataset" />
         </param>
       </when>
     </conditional>