| Previous changeset 0:d3eb4d51b285 (2015-10-10) Next changeset 2:4014cb2c17db (2015-10-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit feb20045fb10de6cce2517784f52672322d4d9f8-dirty |
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modified:
data_manager/hisat2_index_builder.py data_manager/hisat2_index_builder.xml |
| b |
| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 && |