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annotate data_manager/bowtie2_index_builder.xml @ 2:8de13c28d92e draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 10:17:27 -0400
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8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="0.0.2">
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2 <description>builder</description>
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3 <requirements>
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4 <requirement type="package" version="2.2.4">bowtie2</requirement>
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5 </requirements>
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8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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6 <command interpreter="python">bowtie2_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 "bowtie2_indexes" ${tophat2}</command>
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7 <stdio>
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8 <exit_code range=":-1" />
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9 <exit_code range="1:" />
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10 </stdio>
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11 <inputs>
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12 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
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13 <options from_data_table="all_fasta"/>
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14 </param>
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15 <param type="text" name="sequence_name" value="" label="Name of sequence" />
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16 <param type="text" name="sequence_id" value="" label="ID for sequence" />
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8de13c28d92e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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17 <param type="boolean" name="tophat2" label="Also make available for TopHat" checked="True" truevalue="--data_table_name tophat2_indexes" falsevalue="" help="Adds values to tophat2_indexes tool data table." />
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18 </inputs>
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19 <outputs>
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20 <data name="out_file" format="data_manager_json"/>
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21 </outputs>
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22
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23 <help>
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24
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25 .. class:: infomark
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26
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27 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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28
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29 </help>
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30 </tool>