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annotate cpt_convert_mga_to_gff3.xml @ 14:fa68b3ed5407 draft

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author cpt
date Sun, 23 Jul 2023 20:50:22 +0000
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1 <tool id="edu.tamu.cpt2.util.mga_to_gff3" name="MGA to GFF3" version="19.1.0.0">
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2 <description/>
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3 <macros>
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4 <import>cpt-macros.xml</import>
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5 <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">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 @GENOME_SELECTOR_PRE@
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14 python '$__tool_directory__/cpt_convert_mga_to_gff3.py'
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15 '$mga'
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16 @GENOME_SELECTOR@
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17 > '$data' ]]>
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18 </command>
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19 <inputs>
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20 <param label="MGA Output" name="mga" type="data" format="txt"/>
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21 <expand macro="genome_selector"/>
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22 </inputs>
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23 <outputs>
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24 <data format="gff3" name="data">
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25 </data>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="reference_genome_source" value="history"/>
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30 <param name="genome_fasta" value="ConvMga_In.fa"/>
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31 <param name="mga" value="ConvMga_In.out"/>
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32 <output name="data" file="ConvMga_Out.gff3"/>
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33 </test>
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34 </tests>
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35 <help>
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36 **What it does**
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37
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38 Converts an input MetaGeneAnnotator table to the GFF3 format.
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39 </help>
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40 <expand macro="citations"/>
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41 </tool>