Mercurial > repos > cpt > cpt_export_seq_unique

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author cpt
date Fri, 05 Jan 2024 05:50:42 +0000
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1 <tool id="edu.tamu.cpt.gff3.export_seq_unique" name="Feature Sequence Export Unique" version="1.2">
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2 <description>specially modified for sending CDSs to blast</description>
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3 <macros>
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4 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 @GENOME_SELECTOR_PRE@
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11 '$__tool_directory__/gff3_extract_sequence.py'
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12 @GENOME_SELECTOR@
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14 @INPUT_GFF@
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16 --feature_filter unique_cds
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17 '$nodesc'
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18 > '$default'
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19 2> '$gff3'
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20 ]]></command>
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21 <inputs>
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22 <expand macro="genome_selector"/>
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23 <expand macro="gff3_input"/>
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24 <param label="Remove description (use if blasting)" name="nodesc" type="boolean" truevalue="--nodesc" falsevalue=""/>
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25 </inputs>
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26 <outputs>
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27 <data format="fasta" hidden="false" name="default"/>
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28 <data format="gff3" hidden="false" name="gff3"/>
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29 </outputs>
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30 <help><![CDATA[
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31 **What it does**
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32
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33 Extract fasta sequences from a parent genome.
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34 ]]></help>
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35 <expand macro="citations"/>
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36 </tool>