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1 <tool id="plasmid_profiler" name="Plasmid Profiler" version="0.1.6.1">
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0
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2 <description>Explores plasmid content in WGS data</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.6">r-plasmidprofiler</requirement>
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5 <requirement type="package" version="1.3.2">r-optparse</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Error" />
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9 </stdio>
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10 <command>
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11 Rscript '${__tool_directory__}/plasmidprofile.R' --blastfile $blastfile --srst2file $srst2file
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12 #if $sureness != 0.0
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13 --sureness $sureness
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14 #end if
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15 #if $length != 0
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16 --length $length
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17 #end if
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18 $anonymize $combineincs
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19 #if $coverage != 0
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20 --coverage $coverage
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21 #end if
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22 --title "$title" --outfile out
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23 </command>
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24
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25 <inputs>
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26 <param name="blastfile" type="data" format="tabular" label="BLAST TSV file" optional="false" />
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27 <param name="srst2file" type="data" format="tabular" label="SRST2 TSV file" optional="false" />
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28 <param name="sureness" type="float" label="Sureness cut off" value="0" />
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29 <param name="length" type="integer" label="Plasmid length cut off" value="0" />
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30 <param name="coverage" type="integer" label="Percent coverage cut off" value="0" />
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31 <param name="title" type="text" label="Plot title" value="" />
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32 <param name="anonymize" type="boolean" checked="false" label="Anonymize plasmid and sample names" truevalue="--anonymize" falsevalue="" />
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33 <param name="combineincs" type="boolean" checked="false" label="Combine very closely related incompatibility groups" truevalue="--combineincs" falsevalue="" />
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34 </inputs>
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35
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36 <outputs>
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37 <data format="png" name="PNGOutput" label="png output" from_work_dir="*.png" />
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38 <data format="html" name="HTMLOutput" label="html output" from_work_dir="*.html" />
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39 <data format="csv" name="CSVOutput" label="csv output" from_work_dir="*.csv" />
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40 </outputs>
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41
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42 <tests>
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43 <test>
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44 <output/>
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45 </test>
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46 </tests>
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47 <help>
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48 What it does
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49 ============
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50
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51 Heatmap display of plasmid content in WGS data
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52
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53 This program parses plasmids identified through SRST2 and BLAST, scores them based on a combined measure of maximized coverage and minimized sequence divergence, and produces visualizations along with tabular results. Best used on results from the workflow "P2 - Plasmid Profiler: SRST2 and BLAST"
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54
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55 Usage
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56 =====
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57
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58 **BLAST TSV file name:**
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59 - Tab separated value table of BLAST results from querying plasmidfinder database with AMR sequences against SRST2 identified plasmids
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60
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61 **SRST2 TSV file name:**
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62 - Tab separated value table of SRST2 results from querying WGS reads against plasmid database
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63
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64 **Sureness cut off:**
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65 - Sureness is the difference between normalized sequence coverage and divergence. It is a unique measure per dataset that informs the user as to the likelihood the identified plasmid is present in their sample. A value of 0.75 is recommended for a first pass with plasmids scoring above 0.95 to be considered as present in the WGS data.
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66
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67 **Plasmid length cut off:**
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68 - Remove all plasmid sequences below this length from results (eg. 10000)
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69
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70 **Percent coverage cut off:**
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71 - Plasmids with read coverage below this percentage will be excluded from the results (eg. 75)
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72
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73 **Plot title:**
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74 - Custom plot title for heatmap
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75
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76 **Anonymize plasmids and sample names:**
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77 - Hide identifiers in final image and replace with "Plasmid #" and "Sample #"
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78
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79 **Combine very closely related incompatibility groups:**
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80 - Collapse subtypes of incompatibility groups. (eg. FII(S) and FII(K) collapsed to FII)
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81
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82
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83 **Acknowledgments**
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84 Plasmid Profiler Author: Adrian Zetner
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85
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86 Galaxy tool author: Jen Cabral
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87
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88 </help>
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89 <citations>
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90 </citations>
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91 </tool>
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