Mercurial > repos > iuc > data_manager_hisat2_index_builder
diff data_manager/hisat2_index_builder.xml @ 2:16017577fa08 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 4a5952b2404c0821cf9895cb2a5036da62b14d6e-dirty
| author | iuc |
|---|---|
| date | Sat, 10 Oct 2015 16:24:06 -0400 |
| parents | 56f435c0b83e |
| children | a9a26db6a455 |
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--- 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 @@ <exit_code range="1:" /> </stdio> <command><![CDATA[ - #if $advanced.adv_param_select == 'yes' and $gtf_input: - ln -s "${gtf_input}" gtf_file.gtf && + #if $advanced.adv_param_select == 'yes' and $advanced.gtf_input: + ln -s "${advanced.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 $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}"