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annotate generate-putative-isp.xml @ 4:bc16792ecfd2 draft

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author cpt
date Wed, 18 Sep 2024 04:25:38 +0000
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1 <tool id="edu.tamu.cpt2.spanin.generate-putative-isp" name="ISP candidates" version="1.0">
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2 <description>constructs a putative list of potential i-spanin from an input genomic FASTA</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="2019.06.08">regex</requirement>
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8 </expand>
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9 <command detect_errors="aggressive"><![CDATA[
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10 python '$__tool_directory__/generate-putative-isp.py'
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11 '$fasta_file'
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12 --strand '$strand'
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13 --switch '$switch'
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14 --isp_on '$isp_on'
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15 --isp_op '$isp_op'
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16 --isp_ob '$isp_ob'
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17 --isp_og '$isp_og'
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18 --isp_min_len '$isp_min_len'
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19 --isp_min_dist '$isp_min_dist'
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20 --isp_max_dist '$isp_max_dist'
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21 --min_tmd_size '$min_tmd_size'
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22 --max_tmd_size '$max_tmd_size'
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23 --putative_isp '$putative_isp'
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24 --summary_isp_txt '$summary_isp'
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25 --putative_isp_gff '$putative_isp_gff'
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26 --isp_max '$isp_max'
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27 --peri_min '$peri_min'
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28 --peri_max '$peri_max'
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29
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30 ]]></command>
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31 <inputs>
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32 <param type="select" label="Strand Choice" name="strand">
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33 <option value="both">both</option>
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34 <option value="forward">+</option>
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35 <option value="reverse">-</option>
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36 </param>
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37 <param label="Single Genome FASTA" name="fasta_file" type="data" format="fasta"/>
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38 <param label="i-spanin minimal length" name="isp_min_len" type="integer" value="60"/>
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39 <param label="i-spanin maximum length" name="isp_max" type="integer" value="230"/>
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40 <param label="Range Selection; default is all; for a specific range to check for a spanin input integers separated by a colon (eg. 1000:2000)" type="text" name="switch" value="all"/>
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41 <param label="TMD minimal distance from start codon" name="isp_min_dist" type="integer" value="10"/>
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42 <param label="TMD maximum distance from start codon" name="isp_max_dist" type="integer" value="35" help="Searches for a TMD between TMDmin and TMDmax ie [TMDmin,TMDmax]"/>
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43 <param label="TMD minimal size" name="min_tmd_size" type="integer" value="10"/>
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44 <param label="TMD maximum size" name="max_tmd_size" type="integer" value="25"/>
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45 <param label="Periplasmic minimal residue amount" name="peri_min" type="integer" value="16"/>
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46 <param label="Periplasmic maximum residue amount" name="peri_max" type="integer" value="206"/>
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47 </inputs>
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48 <outputs>
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49 <data format="fasta" name="isp_on" label="NucSequences.fa" hidden="true"/>
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50 <data format="fasta" name="isp_op" label="ProtSequences.fa" hidden="true"/>
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51 <data format="bed" name="isp_ob" label="BED_Output.bed" hidden="true"/>
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52 <data format="gff3" name="isp_og" label="GFF_Output.gff" hidden="true"/>
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53 <data format="fasta" name="putative_isp" label="putative_isp.fa"/>
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54 <data format="txt" name="summary_isp" label="summary_isp.txt"/>
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55 <data format="gff3" name="putative_isp_gff" label="putative_isp.gff3"/>
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56 </outputs>
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57 <help><![CDATA[
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58
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59 **What it does**
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60 Searches a genome for candidate i-spanins (ISPs), a phage protein involved in outer membrane disruption during Gram-negative bacterial host cell lysis.
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61
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62 **METHODOLOGY**
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63
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64 Locates ALL potential start sequences, based on TTG / ATG / GTG (M / L / V). This list is pared down to those within the user-set min/max lengths. That filtered list generates a set of files with the ORFs in FASTA (nt and aa), BED, and GFF3 file formats.
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65
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66 With the protein FASTA, the tool next reads in each potential sequence and determines if it has a putative transmembrane domain (TMD) with the following criteria:
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67
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68 1. Presence of snorkeling Lysine residues surrounded by hydrophobic residues described for TMD below, within the range the user specifies.
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69 2. A putative transmembrane domain, or TMD, defined as a repeated hydrophobic region within the sequence ([FIWLVMYCATGSP]), of length and position within the range the user inputs.
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70 3. Length of expected periplasmic region. User defines minimum and maximum thresholds for required number of residues after TMD.
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71
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72 **INPUT** --> Genomic FASTA
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73 *NOTE: This tool only takes a SINGLE genomic fasta. It does not work with multiFASTAs.*
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74
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75 **OUTPUT** --> putative_isp.fa (FASTA) file, putative_isp.gff3, and basic summary statistics as summary_isp.txt.
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76
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77 Protein sequences which passed the above filters are returned as the candidate ISPs.
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78
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79 ]]></help>
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80 <expand macro="citations-crr"/>
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81 </tool>