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annotate data_manager/bowtie2_index_builder.xml @ 4:d1d5feb31804 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 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
author iuc
date Thu, 09 May 2019 16:15:47 -0400
parents 83da94c0e4a6
children 115f3e61b012
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d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
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1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@" profile="18.09">
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2 <description>builder</description>
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3 <requirements>
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iuc
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4 <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement>
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5 </requirements>
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d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
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6 <macros>
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
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7 <token name="@WRAPPER_VERSION@">2.3.4.3</token>
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
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8 </macros>
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83da94c0e4a6 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 <command detect_errors="exit_code"><![CDATA[
83da94c0e4a6 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 python '$__tool_directory__/bowtie2_index_builder.py'
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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11 '${out_file}'
83da94c0e4a6 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 --fasta_filename '${all_fasta_source.fields.path}'
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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13 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
83da94c0e4a6 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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14 --fasta_description '${all_fasta_source.fields.name}'
83da94c0e4a6 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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15 --data_table_name bowtie2_indexes ${tophat2}
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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16 ]]></command>
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17 <inputs>
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18 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
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19 <options from_data_table="all_fasta"/>
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20 </param>
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83da94c0e4a6 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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21 <param name="sequence_name" type="text" value="" label="Name of sequence" />
83da94c0e4a6 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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22 <param name="sequence_id" type="text" value="" label="ID for sequence" />
83da94c0e4a6 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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23 <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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24 </inputs>
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25 <outputs>
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26 <data name="out_file" format="data_manager_json"/>
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27 </outputs>
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28 <tests>
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
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29 <test>
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
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30 <param name="all_fasta_source" value="phiX174"/>
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
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31 <output name="out_file" value="bowtie2_data_manager.json"/>
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
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32 </test>
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
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33 </tests>
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34
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35 <help>
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36 .. class:: infomark
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37
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83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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38 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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39 </help>
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40 </tool>