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Add abspath value translation to data_manager_conf.xml.
author Daniel Blankenberg <dan@bx.psu.edu>
date Tue, 04 Jun 2013 14:57:17 -0400
parents 11e84434ae70
children
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1 <tool id="bwa_index_builder_data_manager" name="BWA index" tool_type="manage_data" version="0.0.1">
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2 <description>builder</description>
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3 <requirements>
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4 <requirement type="package" version="0.5.9">bwa</requirement>
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5 </requirements>
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6 <command interpreter="python">bwa_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "bwa_indexes"</command>
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7 <inputs>
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8 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
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9 <options from_data_table="all_fasta"/>
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10 </param>
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11 <param type="text" name="sequence_name" value="" label="Name of sequence" />
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12 <param type="text" name="sequence_id" value="" label="ID for sequence" />
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13
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14 <param name="index_algorithm" type="select" label="Algorithm for constructing BWT index">
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15 <option value="automatic" selected="True" help="1GB cut-off">Guess automatically</option>
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16 <option value="is" hel="Small genomes">IS linear-time algorithm</option>
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17 <!-- <option value="div">div</option> -->
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18 <option value="bwtsw" help="Large genomes">BWT-SW</option>
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19 </param>
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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
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28 .. class:: infomark
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29
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30 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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32 </help>
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33 </tool>