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1 <tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.9.1">
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2 <description>index builder</description>
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3 <requirements>
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6
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4 <requirement type="package" version="0.11.2">salmon</requirement>
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5 </requirements>
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6
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6 <macros>
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7 <token name="@IDX_VERSION@">q5</token>
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8 </macros>
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9 <command detect_errors="exit_code"><![CDATA[
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10 python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}'
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11 --fasta_filename '${all_fasta_source.fields.path}'
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12 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
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13 --fasta_description '${all_fasta_source.fields.name}'
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14 --kmer_size "${kmer_size}"
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15 --data_table_name salmon_indexes_versioned
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16 --index_version @IDX_VERSION@
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
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21 <options from_data_table="all_fasta" />
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22 </param>
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23 <param name="sequence_name" type="text" value="" label="Name of sequence" />
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24 <param name="sequence_id" type="text" value="" label="ID for sequence" />
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25 <param name="kmer_size" type="integer" optional='true' value="21" max="32" label="The size of the k-mer on which the index is built"
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26 help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be. We generally recommend using a k-mer size of at least 20. MUST BE AN ODD VALUE "/>
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27
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28
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29
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30 </inputs>
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31 <outputs>
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32 <data name="out_file" format="data_manager_json" />
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33 </outputs>
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34 <help>
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35 <![CDATA[
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36 .. class:: infomark
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37
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38 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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39 ]]>
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40 </help>
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41 </tool>
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42
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