# HG changeset patch
# User iuc
# Date 1444508646 14400
# Node ID 16017577fa084b757795653d75071bf9a686c956
# Parent 56f435c0b83e0d7d53f6d2613eb4aaf0e4080cb3
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 4a5952b2404c0821cf9895cb2a5036da62b14d6e-dirty
diff -r 56f435c0b83e -r 16017577fa08 data_manager/hisat2_index_builder.xml
--- a/data_manager/hisat2_index_builder.xml Sat Oct 10 16:00:23 2015 -0400
+++ b/data_manager/hisat2_index_builder.xml Sat Oct 10 16:24:06 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}"