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author cpt
date Fri, 05 Jan 2024 05:51:12 +0000
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1 <tool id="edu.tamu.cpt.external.aragorn-gff3" name="Fix tRNA model" version="19.1.0.0">
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2 <description/>
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3 <macros>
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4 <import>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 '$__tool_directory__/fix-aragorn-gff3.py'
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14 @INPUT_GFF@
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15 > '$default']]></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="default"/>
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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="FixAra_In.gff3"/>
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25 <output name="default" file="FixAra_Out.gff3"/>
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26 </test>
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27 </tests>
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28 <help><![CDATA[
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29 **What it does**
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31 For an input GFF3 file with tRNAs from the Aragorn or converted from the tRNAscan-SE tools, this tool modifies
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32 the gene model to reflect a gene-tRNA-exon hierarchy. That change is needed
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33 to allow for creation of proper tRNA features in Apollo.
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34 ]]></help>
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35 <expand macro="citations"/>
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36 </tool>