Mercurial > repos > ieguinoa > data_manager_salmon_index_builder

comparison data_manager/salmon_index_builder.xml @ 6:d22f69a2e80e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author ieguinoa
date Tue, 23 Jul 2019 09:25:04 -0400
parents c5dea2080109
children cbe62bd6e149
comparison
equal deleted inserted replaced
5:3888ec1918d0 6:d22f69a2e80e
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" />