Mercurial > repos > iuc > data_manager_bowtie_index_builder

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit a54e50916ebdb0858b049cdc549a43df801e1a71
author iuc
date Tue, 21 May 2024 07:35:37 +0000
parents 86e9af693a33
children
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39a922d01b0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit a54e50916ebdb0858b049cdc549a43df801e1a71
iuc
parents: 4
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1 <tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="1.2.1" profile="23.0">
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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2 <description>builder</description>
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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3 <requirements>
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86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
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4 <requirement type="package" version="1.2.0">bowtie</requirement>
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39a922d01b0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit a54e50916ebdb0858b049cdc549a43df801e1a71
iuc
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5 <requirement type="package" version="3.8.3">python</requirement>
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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6 </requirements>
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86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
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7 <command detect_errors="exit_code"><![CDATA[
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
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8 python '$__tool_directory__/bowtie_index_builder.py'
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
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9 '${out_file}'
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
parents: 2
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10 --fasta_filename '${all_fasta_source.fields.path}'
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
parents: 2
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11 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
parents: 2
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12 --fasta_description '${all_fasta_source.fields.name}'
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
parents: 2
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13 --data_table_name bowtie_indexes
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
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14 ]]></command>
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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15 <inputs>
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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16 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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17 <options from_data_table="all_fasta"/>
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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18 </param>
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86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
parents: 2
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19 <param name="sequence_name" type="text" value="" label="Name of sequence" help="Leave blank to use all_fasta name" />
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
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parents: 2
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20 <param name="sequence_id" type="text" value="" label="ID for sequence" help="Leave blank to use all_fasta id" />
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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21 </inputs>
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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22 <outputs>
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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23 <data name="out_file" format="data_manager_json"/>
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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24 </outputs>
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86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
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25 <help><![CDATA[
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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26 .. class:: infomark
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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27
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86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
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28 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
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29 ]]></help>
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
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30 <citations>
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
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31 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
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32 </citations>
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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33 </tool>