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comparison plasmid_profiler.xml @ 0:885bdc903475 draft

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author nml
date Fri, 03 Feb 2017 16:33:51 -0500
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1 <tool id="plasmid_profiler" name="Plasmid Profiler" version="0.1.6">
2 <description>Explores plasmid content in WGS data</description>
3 <requirements>
4 <requirement type="package" version="3.3.1">r</requirement>
5 <requirement type="package" version="7.45.0">curl</requirement>
6 <requirement type="package" version="0.1.6">r-plasmidprofiler</requirement>
7 <requirement type="package" version="1.3.2">r-optparse</requirement>
8 </requirements>
9 <stdio>
10 <exit_code range="1:" level="fatal" description="Error" />
11 </stdio>
12 <command>
13 Rscript '${__tool_directory__}/plasmidprofile.R' --blastfile $blastfile --srst2file $srst2file
14 #if $sureness != 0.0
15 --sureness $sureness
16 #end if
17 #if $length != 0
18 --length $length
19 #end if
20 $anonymize $combineincs
21 #if $coverage != 0
22 --coverage $coverage
23 #end if
24 --title "$title" --outfile out
25 </command>
26
27 <inputs>
28 <param name="blastfile" type="data" format="tabular" label="BLAST TSV file" optional="false" />
29 <param name="srst2file" type="data" format="tabular" label="SRST2 TSV file" optional="false" />
30 <param name="sureness" type="float" label="Sureness cut off" value="0" />
31 <param name="length" type="integer" label="Plasmid length cut off" value="0" />
32 <param name="coverage" type="integer" label="Percent coverage cut off" value="0" />
33 <param name="title" type="text" label="Plot title" value="" />
34 <param name="anonymize" type="boolean" checked="false" label="Anonymize plasmid and sample names" truevalue="--anonymize" falsevalue="" />
35 <param name="combineincs" type="boolean" checked="false" label="Combine very closely related incompatibility groups" truevalue="--combineincs" falsevalue="" />
36 </inputs>
37
38 <outputs>
39 <data format="png" name="PNGOutput" label="png output" from_work_dir="*.png" />
40 <data format="html" name="HTMLOutput" label="html output" from_work_dir="*.html" />
41 <data format="csv" name="CSVOutput" label="csv output" from_work_dir="*.csv" />
42 </outputs>
43
44 <tests>
45 <test>
46 <output/>
47 </test>
48 </tests>
49 <help>
50 What it does
51 ============
52
53 Heatmap display of plasmid content in WGS data
54
55 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"
56
57 Usage
58 =====
59
60 **BLAST TSV file name:**
61 - Tab separated value table of BLAST results from querying plasmidfinder database with AMR sequences against SRST2 identified plasmids
62
63 **SRST2 TSV file name:**
64 - Tab separated value table of SRST2 results from querying WGS reads against plasmid database
65
66 **Sureness cut off:**
67 - 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.
68
69 **Plasmid length cut off:**
70 - Remove all plasmid sequences below this length from results (eg. 10000)
71
72 **Percent coverage cut off:**
73 - Plasmids with read coverage below this percentage will be excluded from the results (eg. 75)
74
75 **Plot title:**
76 - Custom plot title for heatmap
77
78 **Anonymize plasmids and sample names:**
79 - Hide identifiers in final image and replace with "Plasmid #" and "Sample #"
80
81 **Combine very closely related incompatibility groups:**
82 - Collapse subtypes of incompatibility groups. (eg. FII(S) and FII(K) collapsed to FII)
83
84
85 **Acknowledgments**
86 Plasmid Profiler Author: Adrian Zetner
87
88 Galaxy tool author: Jen Cabral
89
90 </help>
91 <citations>
92 </citations>
93 </tool>