Mercurial > repos > cpt > cpt_fix_sixpack

annotate gff3_fix_sixpack.xml @ 4:326429ea1d33 draft

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author cpt
date Sun, 03 Sep 2023 21:00:07 +0000
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1 <tool id="edu.tamu.cpt.gff3.fixsixpack" name="GFF3 Add Gene to CDS for Sixpack" version="19.1.0.0">
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2 <description>Properly formats naive ORF caller output for Apollo</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>cpt-macros.xml</import>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="3.9.16">python</requirement>
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9 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
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10 <requirement type="package" version="1.81">biopython</requirement>
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11 </expand>
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12 <command detect_errors="aggressive"><![CDATA[
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13 '$__tool_directory__/gff3_fix_sixpack.py'
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14 @INPUT_GFF@
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15 > '$output']]></command>
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16 <inputs>
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17 <expand macro="gff3_input"/>
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18 </inputs>
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19 <outputs>
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20 <data format="gff3" name="output"/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="gff3_data" value="miro.gff3"/>
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25 <output name="output" file="miro.6pfix.gff3"/>
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26 </test>
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27 <test>
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28 <param name="gff3_data" value="miro.cds.gff3"/>
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29 <output name="output" file="miro.cds6pfix.gff3"/>
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33 **What it does**
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34
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35 This tool **strips ALL the mRNA features** in a GFF3 file. It specifically formats
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36 the output of the naïve ORF call Sixpack such that it will be compatible with
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37 Apollo via JBrowse.
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38
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39 ]]></help>
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40 <expand macro="citations"/>
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41 </tool>