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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
author devteam
date Fri, 06 Nov 2015 14:15:00 -0500
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ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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1 <tool id="bwa_index_builder_data_manager" name="BWA index" tool_type="manage_data" version="0.0.1">
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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2 <description>builder</description>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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3 <requirements>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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4 <requirement type="package" version="0.5.9">bwa</requirement>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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5 </requirements>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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6 <command interpreter="python">bwa_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 "bwa_indexes"</command>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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7 <stdio>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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8 <exit_code range=":-1" />
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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9 <exit_code range="1:" />
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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10 </stdio>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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11 <inputs>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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12 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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13 <options from_data_table="all_fasta"/>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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14 </param>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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15 <param type="text" name="sequence_name" value="" label="Name of sequence" />
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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16 <param type="text" name="sequence_id" value="" label="ID for sequence" />
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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18 <param name="index_algorithm" type="select" label="Algorithm for constructing BWT index">
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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19 <option value="automatic" selected="True" help="1GB cut-off">Guess automatically</option>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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20 <option value="is" hel="Small genomes">IS linear-time algorithm</option>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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21 <!-- <option value="div">div</option> -->
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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22 <option value="bwtsw" help="Large genomes">BWT-SW</option>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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23 </param>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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25 </inputs>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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26 <outputs>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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27 <data name="out_file" format="data_manager_json"/>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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28 </outputs>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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30 <help>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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32 .. class:: infomark
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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34 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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36 </help>
ae10d0ddbbb1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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37 </tool>