# HG changeset patch
# User iuc
# Date 1444507278 14400
# Node ID b13b84cb11b589cec8e0a43d9107d18104616000
# Parent  d3eb4d51b28569017aa958d65c7dfd1ee96f9f35
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit feb20045fb10de6cce2517784f52672322d4d9f8-dirty

diff -r d3eb4d51b285 -r b13b84cb11b5 data_manager/hisat2_index_builder.py
--- a/data_manager/hisat2_index_builder.py	Sat Oct 10 14:53:43 2015 -0400
+++ b/data_manager/hisat2_index_builder.py	Sat Oct 10 16:01:18 2015 -0400
@@ -62,7 +62,7 @@
     parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None )
     parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None )
     parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='hisat2_indexes' )
-    parser.add_argument( '--indexer_options', dest='indexer_options', action='store', type=str, required=True, default=None )
+    parser.add_argument( '--indexer_options', dest='indexer_options', action='store', type=str, default=None )
     options = parser.parse_args()
 
     filename = options.output
diff -r d3eb4d51b285 -r b13b84cb11b5 data_manager/hisat2_index_builder.xml
--- a/data_manager/hisat2_index_builder.xml	Sat Oct 10 14:53:43 2015 -0400
+++ b/data_manager/hisat2_index_builder.xml	Sat Oct 10 16:01:18 2015 -0400
@@ -8,13 +8,13 @@
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-        #if $gtf_input:
+        #if $advanced.adv_param_select == 'yes' and $gtf_input:
             ln -s "${gtf_input}" gtf_file.gtf &&
             python \$HISAT2_ROOT_DIR/bin/extract_splice_sites.py gtf_file.gtf > splice_sites.txt &&
             python \$HISAT2_ROOT_DIR/bin/extract_exons.py gtf_file.gtf > exon.txt &&
             ls -lh &&
         #end if
-        #if $snps:
+        #if $advanced.adv_param_select == 'yes' and $snps:
             ln -s "${all_fasta_source.fields.path}" genome.fa &&
             ln -s "${snps}" snps.tabular &&
             python \$HISAT2_ROOT_DIR/bin/extract_snps.py --genome_file genome.fa --snp_file snps.tabular > snps.txt &&