Mercurial > repos > iuc > data_manager_bowtie_index_builder

annotate data_manager/bowtie_index_builder.xml @ 1:de991e82646a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit e31f6e2900ebbde6f3679882994c761209aeb9e2-dirty
author iuc
date Thu, 15 Sep 2016 03:15:54 -0400
parents ddd44c79a065
children a230fefc187a
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de991e82646a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit e31f6e2900ebbde6f3679882994c761209aeb9e2-dirty
iuc
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1 <tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="0.0.3">
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ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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2 <description>builder</description>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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3 <requirements>
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de991e82646a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit e31f6e2900ebbde6f3679882994c761209aeb9e2-dirty
iuc
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4 <requirement type="package" version="1.1.2">bowtie</requirement>
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ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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5 </requirements>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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6 <command interpreter="python">
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
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7 bowtie_index_builder.py
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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8 "${out_file}"
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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9 --fasta_filename "${all_fasta_source.fields.path}"
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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10 --fasta_dbkey "${all_fasta_source.fields.dbkey}"
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
iuc
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11 --fasta_description "${all_fasta_source.fields.name}"
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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12 --data_table_name "bowtie_indexes"
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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13 </command>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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14 <inputs>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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15 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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16 <options from_data_table="all_fasta"/>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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17 </param>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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18 <param type="text" name="sequence_name" value="" label="Name of sequence" help="Leave blank to use all_fasta name" />
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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19 <param type="text" name="sequence_id" value="" label="ID for sequence" help="Leave blank to use all_fasta id "/>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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20 </inputs>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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21 <outputs>
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22 <data name="out_file" format="data_manager_json"/>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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23 </outputs>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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24 <help>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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26 .. class:: infomark
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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28 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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30 </help>
ddd44c79a065 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 116d4acd35c9357d23f2419cd331b675503916a1-dirty
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31 </tool>