# HG changeset patch
# User sanbi-uwc
# Date 1516882716 18000
# Node ID f4b99437b6b3fc9fda5a78c3e2f99fa9374dd388
# Parent  0b18bb455081c0bd1eb1ca9ee94546aaf5cd1365
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit fa47457b312f36cead164f993d46bcc31d13fe57-dirty

diff -r 0b18bb455081 -r f4b99437b6b3 freebayes.xml
--- a/freebayes.xml	Thu Jan 25 07:13:21 2018 -0500
+++ b/freebayes.xml	Thu Jan 25 07:18:36 2018 -0500
@@ -273,7 +273,6 @@
             <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
                 <option value="cached">Locally cached</option>
                 <option value="history">History</option>
-                <option value="builtin">Built-in</option>
             </param>
             <when value="cached">
                 <expand macro="input_bam">
diff -r 0b18bb455081 -r f4b99437b6b3 leftalign.xml
--- a/leftalign.xml	Thu Jan 25 07:13:21 2018 -0500
+++ b/leftalign.xml	Thu Jan 25 07:18:36 2018 -0500
@@ -32,7 +32,7 @@
             <when value="cached">
                 <param name="input_bam" type="data" format="bam" label="Select alignment file in BAM format">
                     <validator type="unspecified_build" />
-                    <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey"
+                    <validator type="dataset_metadata_in_data_table" table_name="all_fasta" metadata_name="dbkey"
                                metadata_column="1" message="Sequences are not currently available for the specified build." />
                 </param>
                 <param name="ref_file" type="select" label="Using reference genome" argument="--fasta-reference">
diff -r 0b18bb455081 -r f4b99437b6b3 macros.xml
--- a/macros.xml	Thu Jan 25 07:13:21 2018 -0500
+++ b/macros.xml	Thu Jan 25 07:18:36 2018 -0500
@@ -23,7 +23,7 @@
     </xml>
     <xml name="validation">
         <validator type="unspecified_build" />
-        <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
+        <validator type="dataset_metadata_in_data_table" table_name="all_fasta" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
     </xml>
     <xml name="input_bam">
         <conditional name="batchmode">