annotate plasmid_profiler.xml @ 1:fc63bfd55903 draft

Uploaded
author nml
date Fri, 03 Feb 2017 16:34:16 -0500
parents 885bdc903475
children 842d76e75fbe
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
885bdc903475 Uploaded
nml
parents:
diff changeset
1 <tool id="plasmid_profiler" name="Plasmid Profiler" version="0.1.6">
885bdc903475 Uploaded
nml
parents:
diff changeset
2 <description>Explores plasmid content in WGS data</description>
885bdc903475 Uploaded
nml
parents:
diff changeset
3 <requirements>
885bdc903475 Uploaded
nml
parents:
diff changeset
4 <requirement type="package" version="3.3.1">r</requirement>
885bdc903475 Uploaded
nml
parents:
diff changeset
5 <requirement type="package" version="7.45.0">curl</requirement>
885bdc903475 Uploaded
nml
parents:
diff changeset
6 <requirement type="package" version="0.1.6">r-plasmidprofiler</requirement>
885bdc903475 Uploaded
nml
parents:
diff changeset
7 <requirement type="package" version="1.3.2">r-optparse</requirement>
885bdc903475 Uploaded
nml
parents:
diff changeset
8 </requirements>
885bdc903475 Uploaded
nml
parents:
diff changeset
9 <stdio>
885bdc903475 Uploaded
nml
parents:
diff changeset
10 <exit_code range="1:" level="fatal" description="Error" />
885bdc903475 Uploaded
nml
parents:
diff changeset
11 </stdio>
885bdc903475 Uploaded
nml
parents:
diff changeset
12 <command>
885bdc903475 Uploaded
nml
parents:
diff changeset
13 Rscript '${__tool_directory__}/plasmidprofile.R' --blastfile $blastfile --srst2file $srst2file
885bdc903475 Uploaded
nml
parents:
diff changeset
14 #if $sureness != 0.0
885bdc903475 Uploaded
nml
parents:
diff changeset
15 --sureness $sureness
885bdc903475 Uploaded
nml
parents:
diff changeset
16 #end if
885bdc903475 Uploaded
nml
parents:
diff changeset
17 #if $length != 0
885bdc903475 Uploaded
nml
parents:
diff changeset
18 --length $length
885bdc903475 Uploaded
nml
parents:
diff changeset
19 #end if
885bdc903475 Uploaded
nml
parents:
diff changeset
20 $anonymize $combineincs
885bdc903475 Uploaded
nml
parents:
diff changeset
21 #if $coverage != 0
885bdc903475 Uploaded
nml
parents:
diff changeset
22 --coverage $coverage
885bdc903475 Uploaded
nml
parents:
diff changeset
23 #end if
885bdc903475 Uploaded
nml
parents:
diff changeset
24 --title "$title" --outfile out
885bdc903475 Uploaded
nml
parents:
diff changeset
25 </command>
885bdc903475 Uploaded
nml
parents:
diff changeset
26
885bdc903475 Uploaded
nml
parents:
diff changeset
27 <inputs>
885bdc903475 Uploaded
nml
parents:
diff changeset
28 <param name="blastfile" type="data" format="tabular" label="BLAST TSV file" optional="false" />
885bdc903475 Uploaded
nml
parents:
diff changeset
29 <param name="srst2file" type="data" format="tabular" label="SRST2 TSV file" optional="false" />
885bdc903475 Uploaded
nml
parents:
diff changeset
30 <param name="sureness" type="float" label="Sureness cut off" value="0" />
885bdc903475 Uploaded
nml
parents:
diff changeset
31 <param name="length" type="integer" label="Plasmid length cut off" value="0" />
885bdc903475 Uploaded
nml
parents:
diff changeset
32 <param name="coverage" type="integer" label="Percent coverage cut off" value="0" />
885bdc903475 Uploaded
nml
parents:
diff changeset
33 <param name="title" type="text" label="Plot title" value="" />
885bdc903475 Uploaded
nml
parents:
diff changeset
34 <param name="anonymize" type="boolean" checked="false" label="Anonymize plasmid and sample names" truevalue="--anonymize" falsevalue="" />
885bdc903475 Uploaded
nml
parents:
diff changeset
35 <param name="combineincs" type="boolean" checked="false" label="Combine very closely related incompatibility groups" truevalue="--combineincs" falsevalue="" />
885bdc903475 Uploaded
nml
parents:
diff changeset
36 </inputs>
885bdc903475 Uploaded
nml
parents:
diff changeset
37
885bdc903475 Uploaded
nml
parents:
diff changeset
38 <outputs>
885bdc903475 Uploaded
nml
parents:
diff changeset
39 <data format="png" name="PNGOutput" label="png output" from_work_dir="*.png" />
885bdc903475 Uploaded
nml
parents:
diff changeset
40 <data format="html" name="HTMLOutput" label="html output" from_work_dir="*.html" />
885bdc903475 Uploaded
nml
parents:
diff changeset
41 <data format="csv" name="CSVOutput" label="csv output" from_work_dir="*.csv" />
885bdc903475 Uploaded
nml
parents:
diff changeset
42 </outputs>
885bdc903475 Uploaded
nml
parents:
diff changeset
43
885bdc903475 Uploaded
nml
parents:
diff changeset
44 <tests>
885bdc903475 Uploaded
nml
parents:
diff changeset
45 <test>
885bdc903475 Uploaded
nml
parents:
diff changeset
46 <output/>
885bdc903475 Uploaded
nml
parents:
diff changeset
47 </test>
885bdc903475 Uploaded
nml
parents:
diff changeset
48 </tests>
885bdc903475 Uploaded
nml
parents:
diff changeset
49 <help>
885bdc903475 Uploaded
nml
parents:
diff changeset
50 What it does
885bdc903475 Uploaded
nml
parents:
diff changeset
51 ============
885bdc903475 Uploaded
nml
parents:
diff changeset
52
885bdc903475 Uploaded
nml
parents:
diff changeset
53 Heatmap display of plasmid content in WGS data
885bdc903475 Uploaded
nml
parents:
diff changeset
54
885bdc903475 Uploaded
nml
parents:
diff changeset
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"
885bdc903475 Uploaded
nml
parents:
diff changeset
56
885bdc903475 Uploaded
nml
parents:
diff changeset
57 Usage
885bdc903475 Uploaded
nml
parents:
diff changeset
58 =====
885bdc903475 Uploaded
nml
parents:
diff changeset
59
885bdc903475 Uploaded
nml
parents:
diff changeset
60 **BLAST TSV file name:**
885bdc903475 Uploaded
nml
parents:
diff changeset
61 - Tab separated value table of BLAST results from querying plasmidfinder database with AMR sequences against SRST2 identified plasmids
885bdc903475 Uploaded
nml
parents:
diff changeset
62
885bdc903475 Uploaded
nml
parents:
diff changeset
63 **SRST2 TSV file name:**
885bdc903475 Uploaded
nml
parents:
diff changeset
64 - Tab separated value table of SRST2 results from querying WGS reads against plasmid database
885bdc903475 Uploaded
nml
parents:
diff changeset
65
885bdc903475 Uploaded
nml
parents:
diff changeset
66 **Sureness cut off:**
885bdc903475 Uploaded
nml
parents:
diff changeset
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.
885bdc903475 Uploaded
nml
parents:
diff changeset
68
885bdc903475 Uploaded
nml
parents:
diff changeset
69 **Plasmid length cut off:**
885bdc903475 Uploaded
nml
parents:
diff changeset
70 - Remove all plasmid sequences below this length from results (eg. 10000)
885bdc903475 Uploaded
nml
parents:
diff changeset
71
885bdc903475 Uploaded
nml
parents:
diff changeset
72 **Percent coverage cut off:**
885bdc903475 Uploaded
nml
parents:
diff changeset
73 - Plasmids with read coverage below this percentage will be excluded from the results (eg. 75)
885bdc903475 Uploaded
nml
parents:
diff changeset
74
885bdc903475 Uploaded
nml
parents:
diff changeset
75 **Plot title:**
885bdc903475 Uploaded
nml
parents:
diff changeset
76 - Custom plot title for heatmap
885bdc903475 Uploaded
nml
parents:
diff changeset
77
885bdc903475 Uploaded
nml
parents:
diff changeset
78 **Anonymize plasmids and sample names:**
885bdc903475 Uploaded
nml
parents:
diff changeset
79 - Hide identifiers in final image and replace with "Plasmid #" and "Sample #"
885bdc903475 Uploaded
nml
parents:
diff changeset
80
885bdc903475 Uploaded
nml
parents:
diff changeset
81 **Combine very closely related incompatibility groups:**
885bdc903475 Uploaded
nml
parents:
diff changeset
82 - Collapse subtypes of incompatibility groups. (eg. FII(S) and FII(K) collapsed to FII)
885bdc903475 Uploaded
nml
parents:
diff changeset
83
885bdc903475 Uploaded
nml
parents:
diff changeset
84
885bdc903475 Uploaded
nml
parents:
diff changeset
85 **Acknowledgments**
885bdc903475 Uploaded
nml
parents:
diff changeset
86 Plasmid Profiler Author: Adrian Zetner
885bdc903475 Uploaded
nml
parents:
diff changeset
87
885bdc903475 Uploaded
nml
parents:
diff changeset
88 Galaxy tool author: Jen Cabral
885bdc903475 Uploaded
nml
parents:
diff changeset
89
885bdc903475 Uploaded
nml
parents:
diff changeset
90 </help>
885bdc903475 Uploaded
nml
parents:
diff changeset
91 <citations>
885bdc903475 Uploaded
nml
parents:
diff changeset
92 </citations>
885bdc903475 Uploaded
nml
parents:
diff changeset
93 </tool>