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annotate data_manager/bowtie_index_builder.xml @ 4:a230fefc187a 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 67d76bc24ec6a5eb145f05416dc2098999897bae
author iuc
date Fri, 09 Jun 2017 06:11:39 -0400
parents de991e82646a
children a601bb53be5f
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a230fefc187a 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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1 <tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="1.2.0">
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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
iuc
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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
iuc
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3 <requirements>
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a230fefc187a 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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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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5 </requirements>
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a230fefc187a 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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6 <command detect_errors="exit_code"><![CDATA[
a230fefc187a 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 python '$__tool_directory__/bowtie_index_builder.py'
a230fefc187a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
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8 '${out_file}'
a230fefc187a 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 --fasta_filename '${all_fasta_source.fields.path}'
a230fefc187a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
parents: 1
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10 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
a230fefc187a 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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11 --fasta_description '${all_fasta_source.fields.name}'
a230fefc187a 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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12 --data_table_name bowtie_indexes
a230fefc187a 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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13 ]]></command>
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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
iuc
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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
iuc
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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
iuc
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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
iuc
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17 </param>
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a230fefc187a 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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18 <param name="sequence_name" type="text" value="" label="Name of sequence" help="Leave blank to use all_fasta name" />
a230fefc187a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
parents: 1
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19 <param name="sequence_id" type="text" value="" label="ID for sequence" help="Leave blank to use all_fasta id" />
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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
iuc
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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
iuc
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21 <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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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
iuc
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23 </outputs>
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a230fefc187a 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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24 <help><![CDATA[
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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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25 .. 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
iuc
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26
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a230fefc187a 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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27 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
a230fefc187a 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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28 ]]></help>
a230fefc187a 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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29 <citations>
a230fefc187a 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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30 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
a230fefc187a 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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31 </citations>
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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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32 </tool>