<tool id="plasmid_profiler" name="Plasmid Profiler" version="0.1.6">
	<description>Explores plasmid content in WGS data</description>
	<requirements>
		<requirement type="package" version="3.3.1">r</requirement>
		<requirement type="package" version="7.45.0">curl</requirement>
		<requirement type="package" version="0.1.6">r-plasmidprofiler</requirement>
		<requirement type="package" version="1.3.2">r-optparse</requirement>
	</requirements>
	<stdio>
   		<exit_code range="1:"  level="fatal"   description="Error" />
	</stdio>
	<command>
		Rscript '${__tool_directory__}/plasmidprofile.R' --blastfile $blastfile --srst2file $srst2file 
		#if $sureness != 0.0
			--sureness $sureness
		#end if
		#if $length != 0
			--length $length
		#end if
		$anonymize $combineincs 
		#if $coverage != 0
			--coverage $coverage
		#end if
		--title "$title" --outfile out
	</command>

	<inputs>
		<param name="blastfile" type="data" format="tabular" label="BLAST TSV file" optional="false" />
		<param name="srst2file" type="data" format="tabular" label="SRST2 TSV file" optional="false" />
		<param name="sureness" type="float" label="Sureness cut off" value="0" />
		<param name="length" type="integer" label="Plasmid length cut off" value="0" />
		<param name="coverage" type="integer" label="Percent coverage cut off" value="0" />
		<param name="title" type="text" label="Plot title" value="" />
		<param name="anonymize" type="boolean" checked="false" label="Anonymize plasmid and sample names" truevalue="--anonymize" falsevalue="" />
		<param name="combineincs" type="boolean" checked="false" label="Combine very closely related incompatibility groups" truevalue="--combineincs" falsevalue="" />
	</inputs>

	<outputs>
		<data format="png" name="PNGOutput" label="png output" from_work_dir="*.png" />
		<data format="html" name="HTMLOutput" label="html output" from_work_dir="*.html" />
		<data format="csv" name="CSVOutput" label="csv output" from_work_dir="*.csv" />
	</outputs>

	<tests>
		<test>
			<output/>
		</test>
	</tests>
	<help>
What it does
============

Heatmap display of plasmid content in WGS data

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"

Usage
=====

**BLAST TSV file name:**
 - Tab separated value table of BLAST results from querying plasmidfinder database with AMR sequences against SRST2 identified plasmids

**SRST2 TSV file name:**
 - Tab separated value table of SRST2 results from querying WGS reads against plasmid database

**Sureness cut off:**
	- 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. 

**Plasmid length cut off:**
	- Remove all plasmid sequences below this length from results (eg. 10000)

**Percent coverage cut off:**
	- Plasmids with read coverage below this percentage will be excluded from the results (eg. 75)

**Plot title:**
	- Custom plot title for heatmap

**Anonymize plasmids and sample names:**
	- Hide identifiers in final image and replace with "Plasmid #" and "Sample #"

**Combine very closely related incompatibility groups:**
	- Collapse subtypes of incompatibility groups. (eg. FII(S) and FII(K) collapsed to FII)
  

**Acknowledgments**
	Plasmid Profiler Author: Adrian Zetner

	Galaxy tool author: Jen Cabral

    </help>
    <citations>
    </citations>
 </tool>