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1 <?xml version="1.0"?>
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2 <tool id="edu.tamu.cpt.gff3.fixsixpack" name="GFF3 Add Gene to CDS for Sixpack" version="19.1.0.0">
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3 <description>Properly formats naive ORF caller output for Apollo</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 $__tool_directory__/gff3_fix_sixpack.py
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11 @INPUT_GFF@
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12 > $output]]></command>
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13 <inputs>
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14 <expand macro="gff3_input" />
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15 </inputs>
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16 <outputs>
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17 <data format="gff3" name="output"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="gff3_data" value="miro.gff3" />
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22 <output name="output" file="miro.6pfix.gff3" />
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23 </test>
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24 <test>
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25 <param name="gff3_data" value="miro.cds.gff3" />
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26 <output name="output" file="miro.cds6pfix.gff3" />
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 **What it does**
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31
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32 This tool **strips ALL the mRNA features** in a GFF3 file. It specifically formats
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33 the output of the naïve ORF call Sixpack such that it will be compatible with
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34 Apollo via JBrowse.
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35
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36 ]]></help>
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37 <expand macro="citations" />
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38 </tool>
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