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annotate data_manager/bowtie2_index_builder.xml @ 5:8a892275932f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 17:48:28 -0400
parents 49331eedb1c5
children bb050998cee2
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8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="2.3.0">
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2 <description>builder</description>
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3 <requirements>
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8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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4 <requirement type="package" version="2.3.0">bowtie2</requirement>
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5 </requirements>
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8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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6 <command detect_errors="exit_code"><![CDATA[
8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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7 python '$__tool_directory__/bowtie2_index_builder.py'
8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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8 '${out_file}'
8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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9 --fasta_filename '${all_fasta_source.fields.path}'
8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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10 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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11 --fasta_description '${all_fasta_source.fields.name}'
8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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12 --data_table_name bowtie2_indexes ${tophat2}
8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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13 ]]></command>
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14 <inputs>
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15 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
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16 <options from_data_table="all_fasta"/>
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17 </param>
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8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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18 <param name="sequence_name" type="text" value="" label="Name of sequence" />
8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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19 <param name="sequence_id" type="text" value="" label="ID for sequence" />
8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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20 <param name="tophat2" type="boolean" truevalue="--data_table_name tophat2_indexes" falsevalue="" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" />
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21 </inputs>
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22 <outputs>
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23 <data name="out_file" format="data_manager_json"/>
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24 </outputs>
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25
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26 <help>
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27 .. class:: infomark
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28
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8a892275932f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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29 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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30 </help>
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31 </tool>