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Proksee Assemble Galaxy Tool #227

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Proksee Assemble Galaxy Tool #227

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610283f
WIP; issue with quast unable to find joblib
emarinier Jun 15, 2022
14773a1
First pass, depends on fixing config file in Bioconda install.
emarinier Jun 16, 2022
9876dfe
Adding platform to input, contigs to output.
emarinier Jun 16, 2022
66785c5
Updating version.
emarinier Aug 4, 2022
c83a948
Removing unnecessary file.
emarinier Aug 4, 2022
a12cb85
Adding missing shed file.
emarinier Aug 4, 2022
8f393d2
Support for zipped files, better name handling.
emarinier Aug 4, 2022
369187f
Adding test.
emarinier Aug 4, 2022
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9 changes: 9 additions & 0 deletions tools/proksee/.shed.yml
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name: proksee assemble
owner: nml
description: assembles genomes from NGS reads
long_description: a tool for assembling bacterial genomes from NGS reads and evaluating the assemblies using both heuristic and machine learning-based methods
categories:
- Assembly
remote_repository_url: https://github.com/proksee-project/proksee-cmd
homepage_url: https://github.com/proksee-project/proksee-cmd
type: unrestricted
9 changes: 9 additions & 0 deletions tools/proksee/macros.xml
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<?xml version="1.0"?>
<macros>
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">proksee</requirement>
</requirements>
</xml>
<token name="@TOOL_VERSION@">1.0.0a4</token>
</macros>
194 changes: 194 additions & 0 deletions tools/proksee/proksee.xml
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<tool id="proksee_assemble" name="Proksee Assemble" version="1.0.0">
<description>Assembles bacterial genomes from NGS reads and provides an analysis of the assembly.</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
#import re

proksee updatedb &&

#set forward_safe=re.sub('[^\s\w\-.]', '_', str($forward_reads.element_identifier))
ln -s '$forward_reads' '$forward_safe' &&

#if $reverse_reads
#set reverse_safe=re.sub('[^\s\w\-.]', '_', str($reverse_reads.element_identifier))
ln -s '$reverse_reads' '$reverse_safe' &&
#end if

proksee assemble --force -o output '$forward_safe'

#if $reverse_reads
'$reverse_safe'
#end if

#if str($species) != 'auto'
--species '${species}'
#end if

#if str($platform) != 'auto'
--platform '${platform}'
#end if

--memory 8 --threads 4

]]></command>
<inputs>
<param name="forward_reads" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" optional="false" label="Forward or Single-End Reads" />
<param name="reverse_reads" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" optional="true" label="Reverse Reads (Optional)" />
<param name="platform" type="select" label="Sequencing Platform" help="It is best to manually select the sequencing platform if it is known.">
<option value="auto" selected="true">Automatic</option>
<option value="Illumina" selected="true">Illumina</option>
<option value="Ion Torrent" selected="true">Ion Torrent</option>
<option value="Pac Bio" selected="true">Pac Bio</option>
</param>
<param name="species" type="select" label="Species" help="It is best to manually select the species if it is known.">
<option value="auto" selected="true">Automatic</option>
<option value="Acinetobacter baumannii">Acinetobacter baumannii</option>
<option value="Acinetobacter pittii">Acinetobacter pittii</option>
<option value="Bacilli bacterium">Bacilli bacterium</option>
<option value="Bacillus anthracis">Bacillus anthracis</option>
<option value="Bacillus cereus">Bacillus cereus</option>
<option value="Bacillus subtilis">Bacillus subtilis</option>
<option value="Bacillus thuringiensis">Bacillus thuringiensis</option>
<option value="Bacillus velezensis">Bacillus velezensis</option>
<option value="Bacteroidales bacterium">Bacteroidales bacterium</option>
<option value="Bacteroides fragilis">Bacteroides fragilis</option>
<option value="Bacteroides thetaiotaomicron">Bacteroides thetaiotaomicron</option>
<option value="Bifidobacterium adolescentis">Bifidobacterium adolescentis</option>
<option value="Bifidobacterium longum">Bifidobacterium longum</option>
<option value="Bifidobacterium pseudocatenulatum">Bifidobacterium pseudocatenulatum</option>
<option value="Borreliella burgdorferi">Borreliella burgdorferi</option>
<option value="Brucella abortus">Brucella abortus</option>
<option value="Brucella melitensis">Brucella melitensis</option>
<option value="Burkholderia cenocepacia">Burkholderia cenocepacia</option>
<option value="Burkholderia cepacia">Burkholderia cepacia</option>
<option value="Burkholderia gladioli">Burkholderia gladioli</option>
<option value="Burkholderia pseudomallei">Burkholderia pseudomallei</option>
<option value="Burkholderia stagnalis">Burkholderia stagnalis</option>
<option value="Burkholderia ubonensis">Burkholderia ubonensis</option>
<option value="Campylobacter coli">Campylobacter coli</option>
<option value="Campylobacter concisus">Campylobacter concisus</option>
<option value="Campylobacter fetus">Campylobacter fetus</option>
<option value="Campylobacter jejuni">Campylobacter jejuni</option>
<option value="Campylobacter lari">Campylobacter lari</option>
<option value="Citrobacter freundii">Citrobacter freundii</option>
<option value="Clostridiaceae bacterium">Clostridiaceae bacterium</option>
<option value="Clostridiales bacterium">Clostridiales bacterium</option>
<option value="Clostridioides difficile">Clostridioides difficile</option>
<option value="Clostridium beijerinckii">Clostridium beijerinckii</option>
<option value="Clostridium botulinum">Clostridium botulinum</option>
<option value="Clostridium perfringens">Clostridium perfringens</option>
<option value="Clostridium sporogenes">Clostridium sporogenes</option>
<option value="Corynebacterium diphtheriae">Corynebacterium diphtheriae</option>
<option value="Cronobacter sakazakii">Cronobacter sakazakii</option>
<option value="Cutibacterium acnes">Cutibacterium acnes</option>
<option value="Enterobacter asburiae">Enterobacter asburiae</option>
<option value="Enterobacter cloacae">Enterobacter cloacae</option>
<option value="Enterobacter hormaechei">Enterobacter hormaechei</option>
<option value="Enterococcus faecalis">Enterococcus faecalis</option>
<option value="Enterococcus faecium">Enterococcus faecium</option>
<option value="Enterococcus hirae">Enterococcus hirae</option>
<option value="Escherichia albertii">Escherichia albertii</option>
<option value="Escherichia coli">Escherichia coli</option>
<option value="Flavobacteriaceae bacterium">Flavobacteriaceae bacterium</option>
<option value="Flavobacterium psychrophilum">Flavobacterium psychrophilum</option>
<option value="Francisella tularensis">Francisella tularensis</option>
<option value="Haemophilus influenzae">Haemophilus influenzae</option>
<option value="Helicobacter pylori">Helicobacter pylori</option>
<option value="Klebsiella aerogenes">Klebsiella aerogenes</option>
<option value="Klebsiella pneumoniae">Klebsiella pneumoniae</option>
<option value="Klebsiella quasipneumoniae">Klebsiella quasipneumoniae</option>
<option value="Klebsiella variicola">Klebsiella variicola</option>
<option value="Lachnospiraceae bacterium">Lachnospiraceae bacterium</option>
<option value="Lacticaseibacillus paracasei">Lacticaseibacillus paracasei</option>
<option value="Lactiplantibacillus plantarum">Lactiplantibacillus plantarum</option>
<option value="Lactobacillus rhamnosus">Lactobacillus rhamnosus</option>
<option value="Lactococcus lactis">Lactococcus lactis</option>
<option value="Legionella pneumophila">Legionella pneumophila</option>
<option value="Leptospira interrogans">Leptospira interrogans</option>
<option value="Listeria innocua">Listeria innocua</option>
<option value="Listeria monocytogenes">Listeria monocytogenes</option>
<option value="Listeria seeligeri">Listeria seeligeri</option>
<option value="Listeria welshimeri">Listeria welshimeri</option>
<option value="Moraxella catarrhalis">Moraxella catarrhalis</option>
<option value="Mycobacterium avium">Mycobacterium avium</option>
<option value="Mycobacterium tuberculosis">Mycobacterium tuberculosis</option>
<option value="Mycobacteroides abscessus">Mycobacteroides abscessus</option>
<option value="Mycoplasma bovis">Mycoplasma bovis</option>
<option value="Neisseria gonorrhoeae">Neisseria gonorrhoeae</option>
<option value="Neisseria meningitidis">Neisseria meningitidis</option>
<option value="Oenococcus oeni">Oenococcus oeni</option>
<option value="Pasteurella multocida">Pasteurella multocida</option>
<option value="Pediococcus acidilactici">Pediococcus acidilactici</option>
<option value="Proteus mirabilis">Proteus mirabilis</option>
<option value="Pseudomonas aeruginosa">Pseudomonas aeruginosa</option>
<option value="Pseudomonas syringae">Pseudomonas syringae</option>
<option value="Pseudomonas viridiflava">Pseudomonas viridiflava</option>
<option value="Rhizobium leguminosarum">Rhizobium leguminosarum</option>
<option value="Rhodobacteraceae bacterium">Rhodobacteraceae bacterium</option>
<option value="Rhodococcus hoagii">Rhodococcus hoagii</option>
<option value="Ruegeria conchae">Ruegeria conchae</option>
<option value="Salmonella enterica">Salmonella enterica</option>
<option value="Serratia marcescens">Serratia marcescens</option>
<option value="Shigella boydii">Shigella boydii</option>
<option value="Shigella dysenteriae">Shigella dysenteriae</option>
<option value="Shigella flexneri">Shigella flexneri</option>
<option value="Shigella sonnei">Shigella sonnei</option>
<option value="Sinorhizobium meliloti">Sinorhizobium meliloti</option>
<option value="Staphylococcus aureus">Staphylococcus aureus</option>
<option value="Staphylococcus epidermidis">Staphylococcus epidermidis</option>
<option value="Staphylococcus haemolyticus">Staphylococcus haemolyticus</option>
<option value="Staphylococcus pseudintermedius">Staphylococcus pseudintermedius</option>
<option value="Stenotrophomonas maltophilia">Stenotrophomonas maltophilia</option>
<option value="Streptococcus agalactiae">Streptococcus agalactiae</option>
<option value="Streptococcus equi">Streptococcus equi</option>
<option value="Streptococcus mitis">Streptococcus mitis</option>
<option value="Streptococcus mutans">Streptococcus mutans</option>
<option value="Streptococcus pneumoniae">Streptococcus pneumoniae</option>
<option value="Streptococcus pyogenes">Streptococcus pyogenes</option>
<option value="Streptococcus suis">Streptococcus suis</option>
<option value="Turicibacter sanguinis">Turicibacter sanguinis</option>
<option value="Vibrio cholerae">Vibrio cholerae</option>
<option value="Vibrio parahaemolyticus">Vibrio parahaemolyticus</option>
<option value="Vibrio vulnificus">Vibrio vulnificus</option>
<option value="Xanthomonas campestris">Xanthomonas campestris</option>
<option value="Xanthomonas citri">Xanthomonas citri</option>
<option value="Xanthomonas oryzae">Xanthomonas oryzae</option>
<option value="Xanthomonas phaseoli">Xanthomonas phaseoli</option>
<option value="Yersinia enterocolitica">Yersinia enterocolitica</option>
<option value="Yersinia pestis">Yersinia pestis</option>
<option value="Yersinia pseudotuberculosis">Yersinia pseudotuberculosis</option>
</param>
</inputs>
<outputs>
<data format="json" name="assembly_info" from_work_dir="output/assembly_info.json" label="Proksee assembly information" />
<data format="fasta" name="contigs" from_work_dir="output/contigs.fasta" label="Proksee assembly contigs" />
</outputs>
<tests>
<test>
<param name="forward_reads" value="R1.fastq"/>
<param name="reverse_reads" value="R2.fastq"/>
<param name="species" value="Staphylococcus aureus"/>
<param name="platform" value="Illumina"/>
<output name="assembly_info">
<assert_contents>
<has_text_matching expression="FAIL: The assembly length is smaller than expected: 96337."/>
<has_text_matching expression="The probability of the assembly being a good assembly is: 0.03."/>
</assert_contents>
</output>
</test>
</tests>
<help><![CDATA[

Proksee Assemble
================

Proksee is a suite of command line tools for performing genome assembly, evaluation, annotation, and visualization of microbial genomes. Proksee is developed as a collaboration between the Public Health Agency of Canada, the University of Manitoba, and the University of Alberta.

Proksee Assemble is a tool for assembling bacterial genomes from NGS reads and provides an analysis of the assembly. The analysis includes a heuristic-based evaluation, which checks to see if a variety of assembly metrics (N50, L50, length, etc.) individually fall within a range of values derived from publically-available reference assemblies of the same species. Similarly, the Proksee Assemble evaluation includes a machine learning-based, which considers a variety of assembly metrics in unison reports a probability that the Proksee-produced assembly is similar to publically-available reference assemblies of the same species.

]]></help>
</tool>

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