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