Mercurial > repos > iuc > data_manager_sailfish_index_builder
comparison data_manager/bwa_index_builder.xml @ 0:eae04baa35a6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
| author | iuc |
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| date | Tue, 05 Jan 2016 12:58:16 -0500 |
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| -1:000000000000 | 0:eae04baa35a6 |
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| 1 <tool id="sailfish_index_builder_data_manager" name="Sailfish index" tool_type="manage_data" version="0.0.1"> | |
| 2 <description>builder</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.6.3">sailfish</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 sailfish_index_builder.py "${out_file}" | |
| 8 --fasta_filename "${all_fasta_source.fields.path}" | |
| 9 --fasta_dbkey "${all_fasta_source.fields.dbkey}" | |
| 10 --fasta_description "${all_fasta_source.fields.name}" | |
| 11 --data_table_name "sailfish_indexes" | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | |
| 15 <options from_data_table="all_fasta"/> | |
| 16 </param> | |
| 17 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | |
| 18 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | |
| 19 | |
| 20 <param name="index_algorithm" type="select" label="Algorithm for constructing BWT index"> | |
| 21 <option value="automatic" selected="True" help="1GB cut-off">Guess automatically</option> | |
| 22 <option value="is" hel="Small genomes">IS linear-time algorithm</option> | |
| 23 <!-- <option value="div">div</option> --> | |
| 24 <option value="bwtsw" help="Large genomes">BWT-SW</option> | |
| 25 </param> | |
| 26 | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data name="out_file" format="data_manager_json"/> | |
| 30 </outputs> | |
| 31 | |
| 32 <help> | |
| 33 | |
| 34 .. class:: infomark | |
| 35 | |
| 36 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
| 37 | |
| 38 </help> | |
| 39 </tool> |