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1 <?xml version="1.0"?>
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2 <tool id="edu.tamu.cpt.gff3.prepForApollo" name="Prep GFF3 Input for Apollo" version="20.8.0.0">
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3 <description>by ensuring that CDS features have a wrapping exon feature</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_prep_for_apollo.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="ApolloPrep_In.gff3" />
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22 <output name="output" value="ApolloPrep_Out.gff3" />
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23 </test>
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24 </tests>
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25 <help><![CDATA[
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26 **What it does**
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27
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28 This tool updates the gene model in a GFF3 so that it can be added into Apollo
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29 and be used to promote annotations with the correct CDS calculation. It finds any
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30 CDS feature who's direct parent is a gene feature, and creates an exon feature
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31 that is the child of the gene feature and the parent of the CDS. If a gene has
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32 multiple CDS features, they will be wrapped under the same exon feature.
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33
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34 All other features present in the GFF under the gene will be kept the same.
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35
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36 Warning: Use this tool only when it is absolutely necessary to fix a gene model.
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37
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38 ]]></help>
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39 <expand macro="citations-clm" />
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40 </tool>
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