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date Fri, 05 Jan 2024 05:57:00 +0000
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1 <tool id="edu.tamu.cpt.gff3.require_phage_start" name="GFF3 Filter: Require Phage Start" version="19.1.0.0">
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2 <description>ensures start is ATG, TTG, or GTG</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 @GENOME_SELECTOR_PRE@
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15 python '$__tool_directory__/gff3_require_phage_start.py'
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16
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17 @GENOME_SELECTOR@
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18 '$gff3_data'
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20 > '$stdout'
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22 ]]></command>
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23 <inputs>
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24 <expand macro="genome_selector"/>
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25 <expand macro="gff3_input"/>
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26 </inputs>
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27 <outputs>
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28 <data format="gff3" name="stdout" label="$gff3_data.name filtered for start codon"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="reference_genome_source" value="history"/>
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33 <param name="genome_fasta" value="T7_ReqPhageIn.fasta"/>
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34 <param name="gff3_data" value="T7_ReqPhageIn.gff3"/>
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35 <output name="stdout" file="T7_ReqPhageOut.gff3"/>
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36 </test>
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37 <test>
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38 <param name="reference_genome_source" value="history"/>
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39 <param name="genome_fasta" value="Miro_ReqPhageIn.fa"/>
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40 <param name="gff3_data" value="Miro_ReqPhageIn.gff3"/>
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41 <output name="stdout" file="Miro_ReqPhageOut.gff3"/>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 **What it does**
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47 Removes any CDS from the GFF3 whose start codon is **not** ATG, TTG, or GTG.
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48
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49 .. class:: warningmark
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51 The tool only retains *gene* and *CDS* features that pass this filter.
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52 ]]></help>
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53 <expand macro="citations"/>
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54 </tool>