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annotate data_manager/picard_index_builder.xml @ 2:b99040168706 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 59ee07d9786f1a090053b4a13192247872389d61
author iuc
date Mon, 10 Apr 2017 06:06:23 -0400
parents dc28cd6a1d44
children ae080ff506fd
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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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1 <tool id="picard_index_builder_data_manager" name="Picard index" tool_type="manage_data" version="2.7.1">
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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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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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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
iuc
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7 python '$__tool_directory__/picard_index_builder.py'
dc28cd6a1d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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8 '${out_file}'
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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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
iuc
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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
iuc
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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
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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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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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
iuc
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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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24
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25 <help>
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26 .. class:: infomark
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27
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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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28 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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29 </help>
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30 </tool>