Mercurial > repos > jjohnson > data_manager_picard_index_builder
comparison data_manager/picard_index_builder.xml @ 0:ce8e6a5b8830 draft default tip
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| author | jjohnson |
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| date | Tue, 20 Aug 2013 11:12:02 -0400 |
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| -1:000000000000 | 0:ce8e6a5b8830 |
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| 1 <tool id="picard_index_builder_data_manager" name="Picard index" tool_type="manage_data" version="0.0.1"> | |
| 2 <description>builder</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.96">picard</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python">picard_index_builder.py "${out_file}" --jar_path "\$PICARD_JAR_PATH/CreateSequenceDictionary.jar" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "picard_indexes"</command> | |
| 7 <inputs> | |
| 8 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | |
| 9 <options from_data_table="all_fasta"/> | |
| 10 </param> | |
| 11 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | |
| 12 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data name="out_file" format="data_manager_json"/> | |
| 16 </outputs> | |
| 17 | |
| 18 <help> | |
| 19 | |
| 20 .. class:: infomark | |
| 21 | |
| 22 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
| 23 | |
| 24 </help> | |
| 25 </tool> |