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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author iuc
date Sun, 16 Apr 2023 08:31:10 +0000
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ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
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1 <tool id="picard_index_builder_data_manager" name="Picard index" tool_type="manage_data" version="2.7.1+galaxy1" profile="18.09">
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2 <description>builder</description>
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3 <requirements>
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dc28cd6a1d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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4 <requirement type="package" version="2.7.1">picard</requirement>
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5 </requirements>
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iuc
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6 <command detect_errors="exit_code"><![CDATA[
dc28cd6a1d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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7 python '$__tool_directory__/picard_index_builder.py'
dc28cd6a1d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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8 '${out_file}'
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9 --fasta_filename '${all_fasta_source.fields.path}'
dc28cd6a1d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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10 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
dc28cd6a1d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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11 --fasta_description '${all_fasta_source.fields.name}'
dc28cd6a1d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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12 --data_table_name picard_indexes
dc28cd6a1d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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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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18 <param name="sequence_name" type="text" value="" label="Name of sequence" />
dc28cd6a1d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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19 <param name="sequence_id" type="text" value="" label="ID for sequence" />
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20 </inputs>
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21 <outputs>
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22 <data name="out_file" format="data_manager_json"/>
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23 </outputs>
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ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
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24 <tests>
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
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25 <test>
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26 <param name="all_fasta_source" value="phiX174"/>
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
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27 <output name="out_file" value="picard_index_builder_data_manager.json"/>
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
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28 </test>
ae080ff506fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
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29 </tests>
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30 <help>
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31 .. class:: infomark
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32
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33 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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34 </help>
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35 </tool>