Mercurial > repos > devteam > data_manager_gatk_picard_index_builder
comparison data_manager/data_manager_gatk_picard_index_builder.xml @ 0:619dd9e9c09c draft
Imported from capsule None
author | devteam |
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date | Tue, 01 Apr 2014 10:48:03 -0400 |
parents | |
children | 700f2df51eb0 |
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-1:000000000000 | 0:619dd9e9c09c |
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1 <tool id="gatk_picard_index_builder" name="Generate GATK-sorted Picard indexes" tool_type="manage_data" version="0.0.1"> | |
2 <description>builder</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.1.18">samtools</requirement> | |
5 <requirement type="package" version="1.56.0">picard</requirement> | |
6 </requirements> | |
7 <command interpreter="python"> | |
8 data_manager_gatk_picard_index_builder.py "${out_file}" \ | |
9 --jar "\$JAVA_JAR_PATH/CreateSequenceDictionary.jar" \ | |
10 --fasta_filename "${all_fasta_source.fields.path}" \ | |
11 --fasta_dbkey "${all_fasta_source.fields.dbkey}" \ | |
12 --fasta_description "${all_fasta_source.fields.name}" \ | |
13 --data_table_name "gatk_picard_indexes" | |
14 </command> | |
15 <inputs> | |
16 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | |
17 <options from_data_table="all_fasta"/> | |
18 </param> | |
19 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | |
20 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | |
21 </inputs> | |
22 <outputs> | |
23 <data name="out_file" format="data_manager_json"/> | |
24 </outputs> | |
25 | |
26 <help> | |
27 | |
28 .. class:: infomark | |
29 | |
30 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
31 | |
32 </help> | |
33 </tool> |