# HG changeset patch
# User iuc
# Date 1444508630 14400
# Node ID 4014cb2c17db81c972a8e95ccca2b331c32968d2
# Parent b13b84cb11b589cec8e0a43d9107d18104616000
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 4a5952b2404c0821cf9895cb2a5036da62b14d6e-dirty
diff -r b13b84cb11b5 -r 4014cb2c17db data_manager/hisat2_index_builder.xml
--- a/data_manager/hisat2_index_builder.xml Sat Oct 10 16:01:18 2015 -0400
+++ b/data_manager/hisat2_index_builder.xml Sat Oct 10 16:23:50 2015 -0400
@@ -8,15 +8,15 @@
splice_sites.txt &&
python \$HISAT2_ROOT_DIR/bin/extract_exons.py gtf_file.gtf > exon.txt &&
ls -lh &&
#end if
- #if $advanced.adv_param_select == 'yes' and $snps:
+ #if $advanced.adv_param_select == 'yes' and $advanced.snps:
ln -s "${all_fasta_source.fields.path}" genome.fa &&
- ln -s "${snps}" snps.tabular &&
+ ln -s "${advanced.snps}" snps.tabular &&
python \$HISAT2_ROOT_DIR/bin/extract_snps.py --genome_file genome.fa --snp_file snps.tabular > snps.txt &&
#end if
python $__tool_directory__/hisat2_index_builder.py --output "${out_file}"