| Next changeset 1:fc63bfd55903 (2017-02-03) |
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Commit message:
Uploaded |
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added:
plasmid_profiler.xml |
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| diff -r 000000000000 -r 885bdc903475 plasmid_profiler.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plasmid_profiler.xml Fri Feb 03 16:33:51 2017 -0500 |
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| @@ -0,0 +1,93 @@ +<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> |