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1 <?xml version="1.0"?>
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2 <tool id="edu.tamu.cpt.gff3.cdsParents" name="GFF3 Add Gene to CDS" version="19.1.0.0">
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3 <description>is one step of fixing a gene model--adding parent gene features to CDSs</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_add_parents_to_cds.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="T7_AddParentIn.gff3" />
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22 <output name="output">
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23 <assert_contents>
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24 <has_line line="##gff-version 3"/>
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25 <has_n_lines n="10105" />
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26 </assert_contents>
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27 </output>
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28 </test>
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29 <test>
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30 <param name="gff3_data" value="Miro_AddParentIn.gff3" />
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31 <output name="output">
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32 <assert_contents>
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33 <has_line line="##gff-version 3"/>
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34 <has_n_lines n="829" />
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35 </assert_contents>
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36 </output>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 **What it does**
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41
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42 This tool updates the gene model in a GFF3, useful when a nonstandard gene model
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43 has been applied. It finds all CDS features, **strips their parent features**,
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44 then applies a gene-mRNA-CDS model, compliant with the standard GFF3 format.
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45
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46 Warning: Use this tool only when it is absolutely necessary to fix a gene model.
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47
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48 ]]></help>
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49 <expand macro="citations" />
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50 </tool>
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