Mercurial > repos > devteam > data_manager_bowtie2_index_builder
comparison data_manager/bowtie2_index_builder.xml @ 0:9458af1ab90b draft
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author | devteam |
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date | Tue, 14 Apr 2015 12:06:01 -0400 |
parents | |
children | 9bf4eb559ed5 |
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-1:000000000000 | 0:9458af1ab90b |
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1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="0.0.1"> | |
2 <description>builder</description> | |
3 <requirements> | |
4 <requirement type="package" version="2.2.4">bowtie2</requirement> | |
5 </requirements> | |
6 <command interpreter="python">bowtie2_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "bowtie2_indexes"</command> | |
7 <stdio> | |
8 <exit_code range=":-1" /> | |
9 <exit_code range="1:" /> | |
10 </stdio> | |
11 <inputs> | |
12 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | |
13 <options from_data_table="all_fasta"/> | |
14 </param> | |
15 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | |
16 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | |
17 </inputs> | |
18 <outputs> | |
19 <data name="out_file" format="data_manager_json"/> | |
20 </outputs> | |
21 | |
22 <help> | |
23 | |
24 .. class:: infomark | |
25 | |
26 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
27 | |
28 </help> | |
29 </tool> |