Mercurial > repos > iuc > data_manager_hisat2_index_builder
changeset 1:b13b84cb11b5 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit feb20045fb10de6cce2517784f52672322d4d9f8-dirty
| author | iuc |
|---|---|
| date | Sat, 10 Oct 2015 16:01:18 -0400 |
| parents | d3eb4d51b285 |
| children | 4014cb2c17db |
| files | data_manager/hisat2_index_builder.py data_manager/hisat2_index_builder.xml |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- 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
--- 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 &&