Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
comparison data_manager/salmon_index_builder.xml @ 6:d22f69a2e80e draft
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author | ieguinoa |
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date | Tue, 23 Jul 2019 09:25:04 -0400 |
parents | c5dea2080109 |
children | cbe62bd6e149 |
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5:3888ec1918d0 | 6:d22f69a2e80e |
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1 <tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.9.1"> | 1 <tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.9.1"> |
2 <description>index builder</description> | 2 <description>index builder</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.9.1">salmon</requirement> | 4 <requirement type="package" version="0.11.2">salmon</requirement> |
5 </requirements> | 5 </requirements> |
6 <macros> | |
7 <token name="@IDX_VERSION@">q5</token> | |
8 </macros> | |
6 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
7 python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}' | 10 python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}' |
8 --fasta_filename '${all_fasta_source.fields.path}' | 11 --fasta_filename '${all_fasta_source.fields.path}' |
9 --fasta_dbkey '${all_fasta_source.fields.dbkey}' | 12 --fasta_dbkey '${all_fasta_source.fields.dbkey}' |
10 --fasta_description '${all_fasta_source.fields.name}' | 13 --fasta_description '${all_fasta_source.fields.name}' |
11 --kmer_size "${kmer_size}" | 14 --kmer_size "${kmer_size}" |
12 --data_table_name salmon_indexes | 15 --data_table_name salmon_indexes |
16 --index_version @IDX_VERSION@ | |
13 ]]> | 17 ]]> |
14 </command> | 18 </command> |
15 <inputs> | 19 <inputs> |
16 <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> | 20 <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> |
17 <options from_data_table="all_fasta" /> | 21 <options from_data_table="all_fasta" /> |