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1 <?xml version="1.0"?>
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2 <tool id="edu.tamu.cpt.gff3.export_seq_unique" name="Feature Sequence Export Unique" version="1.2">
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3 <description>specially modified for sending CDSs to blast</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>cpt-macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 @GENOME_SELECTOR_PRE@
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11
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12 $__tool_directory__/gff3_extract_sequence.py
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13 @GENOME_SELECTOR@
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14
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15 @INPUT_GFF@
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16
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17 --feature_filter unique_cds
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18 $nodesc
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19 > $default
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20 2> $gff3
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21 ]]></command>
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22 <inputs>
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23 <expand macro="genome_selector" />
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24 <expand macro="gff3_input" />
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25 <param label="Remove description (use if blasting)" name="nodesc" type="boolean" truevalue="--nodesc" falsevalue=""/>
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26 </inputs>
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27 <outputs>
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28 <data format="fasta" hidden="false" name="default"/>
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29 <data format="gff3" hidden="false" name="gff3"/>
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30 </outputs>
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31 <help><![CDATA[
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32 **What it does**
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33
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34 Extract fasta sequences from a parent genome.
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35 ]]></help>
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36 <expand macro="citations" />
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37 </tool>
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