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1 <?xml version="1.0"?>
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2 <tool id="edu.tamu.cpt.external.aragorn-gff3" name="Fix tRNA model" version="19.1.0.0">
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3 <description></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__/fix-aragorn-gff3.py
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11 @INPUT_GFF@
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12 > $default]]></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="default"/>
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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="FixAra_In.gff3"/>
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22 <output name="default" file="FixAra_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 For an input GFF3 file with tRNAs from the Aragorn or converted from the tRNAscan-SE tools, this tool modifies
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29 the gene model to reflect a gene-tRNA-exon hierarchy. That change is needed
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30 to allow for creation of proper tRNA features in Apollo.
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31 ]]></help>
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32 <expand macro="citations" />
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33 </tool>
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