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annotate findSpanin.xml @ 3:fd70980a516b draft

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author cpt
date Mon, 05 Jun 2023 02:42:01 +0000
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1 <tool id="edu.tamu.cpt2.spanin.findSpanin" name="Find Spanin" version="1.0">
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2 <description>With the outputs from the ISP and OSP candidate tools, cull the list down to candidate pairs</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>cpt-macros.xml</import>
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6 </macros>
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7 <expand macro="requirements">
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8 </expand>
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9 <command detect_errors="aggressive"><![CDATA[
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10 python '$__tool_directory__/findSpanin.py'
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11 '$putative_isp_fasta_file'
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12 '$putative_osp_fasta_file'
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13 --max_isp_osp_distance '$max_isp_osp_distance'
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14 --embedded_txt '$embedded_txt'
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15 --overlap_txt '$overlap_txt'
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16 --separate_txt '$separate_txt'
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17 --summary_txt '$summary_txt'
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18 ]]></command>
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19 <inputs>
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20 <param label="(putative) i-spanin FASTA file" name="putative_isp_fasta_file" type="data" format="fasta"/>
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21 <param label="(putative) o-spanin FASTA file" name="putative_osp_fasta_file" type="data" format="fasta"/>
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22 <param label="max distance from end of i-spanin to beginning of o-spanin (measured in AAs)" name="max_isp_osp_distance" type="integer" value="10"/>
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23 </inputs>
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24 <outputs>
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25 <data format="txt" name="summary_txt" label="FindSpanin_summary.txt"/>
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26 <data format="tabular" name="embedded_txt" label="embedded_results.txt"/>
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27 <data format="tabular" name="overlap_txt" label="overlap_results.txt"/>
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28 <data format="tabular" name="separate_txt" label="separate_results.txt"/>
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29 </outputs>
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30 <help><![CDATA[
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31 **What it does**
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32 Compares the protein FASTA files with candidate i-spanins and o-spanins from a genome and matches them into candidate pairs based on position in a strand-aware fashion.
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33
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34 **INPUT** --> Putative i-spanin and o-spanin protein multiFASTAs (generated from the ISP/OSP Candidate Tools).
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35
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36 **METHODOLOGY**
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37 Does a pairwise comparison between candidate i-spanins and o-spanins based on their genomic location, and classifies them into the known bimolecular spanin genetic architectures. Classes are: embedded, overlapping, separated, or NOT a potential pair.
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38
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39 **OUTPUT** --> File with candidate pairs for each bimolecular spanin class and a basic summary statistics file.
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40
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41 ]]></help>
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42 <expand macro="citations-2020"/>
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43 </tool>