view nullarbor.xml @ 3:63ba2e9353bb draft default tip

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty

<tool id="nullarbor" name="nullarbor" version="@VERSION@">
    <description>Pipeline to generate complete public health microbiology reports from sequenced isolates</description>
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="env" />
    <command detect_errors="exit_code"><![CDATA[
        
        nullarbor.pl
        --run
        --cpus '$opt.cpus'

        #if '$opt.verbose'
            '$opt.verbose'
        #end if
        
        --gcode $adv_opt.gcode 

        #if $adv_opt.trim
            $adv_opt.trim
        #end if

        #if str($adv_opt.mlst) != "auto"
            --mlst '$adv_opt.mlst'
        #end if
        
        #if str($adv_opt.snippy_opt) != ""
        --snippy_opt $adv_opt.snippy_opt
        #end if
        
        #if str($adv_opt.roary_opt) != ""
        --roary_opt $adv_opt.roary_opt
        #end if

        #if str($adv_opt.mask) != "AUTO"
        --mask $adv_opt.mask
        #end if

        --assembler $plugins.assembler
        
        #if str($plugins.assembler_opt) != ""
        --assembler_opt $plugins.assembler_opt
        #end if
       
        --treebuilder $plugins.treebuilder
        
        #if str($plugins.treebuilder_opt) != ""
        --treebuilder_opt $plugins.treebuilder_opt
        #end if

        --taxoner $plugins.taxoner
        
        #if str($plugins.taxoner_opt) != ""
        --taxoner_opt $plugins.taxoner_opt
        #end if

        --annotator $plugins.annotator
        
        #if str($plugins.annotator_opt) != ""
        --annotator_opt $plugins.annotator_opt
        #end if

        --name $name 
        --ref $ref 
        --input $tab_file 
        --outdir out 

    ]]></command>

    <inputs>
        <param name="tab_file" format="txt" type="data" label="Tab file generated from nullarbor_prepare" help="You need to run nullarbor_test for generating a tab file of reads before running this tool"/>
        <param name="ref" type="data" format="fasta" label="Reference genome " help="Reference file in FASTA or GBK format"/>
        <param name="name" type="text" optional="False" label="Job name" help="" />
    
        <section name="opt" title="Options">
            <param name="cpus" argument="--cpus" type="integer" value="8" label="CPUs" help="Maximum number of CPUs to use in total (Default: 8)" />
            <param name="verbose" argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose" help="More screen output" />
        </section>

        <section name="adv_opt" title="Advanced Options">
        <param name="gcode" argument="--gcode" type="integer" value="11" label="Genetic code for prokka" help="(Default: 11)" />
        <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" checked="False" label="Trim reads of adaptors" help="(Default: NO)" />
        <param name="mlst" argument="--mlst" type="select" label="Force this MLST scheme" help="(Default: AUTO)">
            <option value="auto">AUTO</option>
            <option value="abaumannii">Acinetobacter baumannii</option>
            <option value="abaumannii_2">Acinetobacter baumannii 2</option>
            <option value="achromobacter">Achromobacter</option>
            <option value="aeromonas">Aeromonas</option>
            <option value="afumigatus">Aspergillus afumigatus</option>
            <option value="aphagocytophilum">Anaplasma aphagocytophilum</option>
            <option value="arcobacter">Arcobacter</option>
            <option value="bburgdorferi">Borrelia  burgdorferi</option>
            <option value="bcc">Burkholderia cepacia</option>
            <option value="bcereus">Bacillus cereus</option>
            <option value="bhampsonii">Brachyspira hampsonii</option>
            <option value="bhenselae">Bartonella henselae</option>
            <option value="bhyodysenteriae">Brachyspira hyodysenteriae</option>
            <option value="bifidobacterium">Bifidobacterium bifidobacterium</option>
            <option value="bintermedia">Brachyspira intermedia</option>
            <option value="blicheniformis">Bacillus licheniformis</option>
            <option value="bordetella">Bordetella pertussis</option>
            <option value="borrelia">Borrelia</option>
            <option value="bpilosicoli">Brachyspira pilosicoli</option>
            <option value="bpseudomallei">Burkholderia pseudomallei</option>
            <option value="brachyspira">Brachyspira</option>
            <option value="bsubtilis">Bacillus subtilis</option>
            <option value="calbicans">Candida albicans</option>
            <option value="campylobacter">Campylobacter coli</option>
            <option value="campylobacter">Campylobacter jejuni</option>
            <option value="cbotulinum">Clostridium botulinum</option>
            <option value="cconcisus">Campylobacter concisus</option>
            <option value="cdifficile">Clostridium difficile</option>
            <option value="cdifficile">Peptoclostridium difficile</option>
            <option value="cdifficile_2">Clostridium difficile 2</option>
            <option value="cdiphtheriae">Corynebacterium diphtheriae</option>
            <option value="cfetus">Campylobacter fetus</option>
            <option value="cfreundii">Citrobacter freundii</option>
            <option value="cglabrata">Candida glabrata</option>
            <option value="chelveticus">Campylobacter helveticus</option>
            <option value="chlamydiales">Chlamydia</option>
            <option value="chyointestinalis">Campylobacter hyointestinalis</option>
            <option value="cinsulaenigrae">Campylobacter insulaenigrae</option>
            <option value="ckrusei">Candida krusei</option>
            <option value="clanienae">Campylobacter lanienae</option>
            <option value="clari">Campylobacter lari</option>
            <option value="cmaltaromaticum">Carnobacterium maltaromaticum</option>
            <option value="cneoformans">Cryptococcus neoformans</option>
            <option value="cronobacter">Cronobacter</option>
            <option value="csepticum">Clostridium septicum</option>
            <option value="csinensis">Clonorchis sinensis</option>
            <option value="csputorum">Campylobacter sputorum</option>
            <option value="ctropicalis">Candida tropicalis</option>
            <option value="cupsaliensis">Campylobacter upsaliensis</option>
            <option value="ecloacae">Enterobacter cloacae</option>
            <option value="ecoli">Escherichia</option>
            <option value="ecoli">Shigella</option>
            <option value="ecoli_2">Escherichia 2</option>
            <option value="edwardsiella">Edwardsiella tarda</option>
            <option value="efaecalis">Enterococcus faecalis</option>
            <option value="efaecium">Enterococcus faecium</option>
            <option value="fpsychrophilum">Flavobacterium psychrophilum</option>
            <option value="haemophilus">Haemophilus</option>
            <option value="hcinaedi">Helicobacter cinaedi</option>
            <option value="hinfluenzae">Haemophilus influenzae</option>
            <option value="hparasuis">Haemophilus parasuis</option>
            <option value="hpylori">Helicobacter pylori</option>
            <option value="hsuis">Haematopinus suis</option>
            <option value="kkingae">Kingella kingae</option>
            <option value="koxytoca">Klebsiella oxytoca</option>
            <option value="kpneumoniae">Klebsiella pneumoniae</option>
            <option value="kseptempunctata">Kudoa septempunctata</option>
            <option value="lcasei">Lactobacillus casei</option>
            <option value="legionella">Legionella</option>
            <option value="leptospira">Leptospira</option>
            <option value="leptospira_2">Leptospira 2</option>
            <option value="leptospira_3">Leptospira 3</option>
            <option value="lmonocytogenes">Listeria monocytogenes</option>
            <option value="lsalivarius">Lactobacillus salivarius</option>
            <option value="mabscessus">Mycobacterium abscessus</option>
            <option value="magalactiae">Mycoplasma agalactiae</option>
            <option value="mbovis">Mycoplasma bovis</option>
            <option value="mcatarrhalis">Moraxells catarrhalis</option>
            <option value="mhaemolytica">Mannheimia haemolytica</option>
            <option value="mhyorhinis">Mycoplasma hyorhinis</option>
            <option value="mmassiliense">Mycobacterium massiliense</option>
            <option value="mplutonius">Melissococcus plutonius</option>
            <option value="neisseria">Neisseria</option>
            <option value="orhinotracheale">Ornithobacterium rhinotracheale</option>
            <option value="otsutsugamushi">Orientia tsutsugamushi</option>
            <option value="pacnes">Propionibacterium acnes</option>
            <option value="paeruginosa">Pseudomonas aeruginosa</option>
            <option value="pagglomerans">Pantoea agglomerans</option>
            <option value="pfluorescens">Pseudomonas fluorescens</option>
            <option value="pfreudenreichii">Propionibacterium freudenreichii</option>
            <option value="pgingivalis">Porphyromonas gingivalis</option>
            <option value="plarvae">Paenibacillus larvae</option>
            <option value="pmultocida_multihost">Pasteurella multocida</option>
            <option value="pmultocida_rirdc">Pasteurella multocida</option>
            <option value="ppentosaceus">Pediococcus pentosaceus</option>
            <option value="pshigelloides">Plesiomonas shigelloides</option>
            <option value="ranatipestifer">Riemerella anatipestifer</option>
            <option value="sagalactiae">Streptococcus agalactiae</option>
            <option value="saureus">Staphylococcus aureus</option>
            <option value="scanis">Streptococcus canis</option>
            <option value="sdysgalactiae">Streptococcus dysgalactiae</option>
            <option value="senterica">Salmonella  enterica</option>
            <option value="sepidermidis">Staphylococcus  epidermidis</option>
            <option value="sgallolyticus">Streptococcus gallolyticus</option>
            <option value="shaemolyticus">Staphylococcus  haemolyticus</option>
            <option value="shominis">Stapylococcus hominis</option>
            <option value="sinorhizobium">Sinorhizobium</option>
            <option value="slugdunensis">Staphylococcus  lugdunensis</option>
            <option value="smaltophilia">Stenotrophomonas  maltophilia</option>
            <option value="soralis">Streptococcus oralis</option>
            <option value="spneumoniae">Streptococcus pneumoniae</option>
            <option value="spseudintermedius">Staphylococcus  pseudintermedius</option>
            <option value="spyogenes">Streptococcus pyogenes</option>
            <option value="ssuis">Streptococcus suis</option>
            <option value="sthermophilus">Streptococcus thermophilus</option>
            <option value="sthermophilus_2">Streptococcus thermophilus 2</option>
            <option value="streptomyces">Streptomyces</option>
            <option value="suberis">Streptococcus uberis</option>
            <option value="szooepidemicus">Streptococcus equi</option>
            <option value="taylorella">Taylorella</option>
            <option value="tenacibaculum">Tenacibaculum</option>
            <option value="tvaginalis">Trichomonas vaginalis</option>
            <option value="vcholerae">Vibrio  cholerae</option>
            <option value="vibrio">Vibrio</option>
            <option value="vparahaemolyticus">Vibrio  parahaemolyticus</option>
            <option value="vtapetis">Vibrio tapetis</option>
            <option value="vvulnificus">Vibrio  vulnificus</option>
            <option value="wolbachia">Wolbachia</option>
            <option value="xfastidiosa">Xylella fastidiosa</option>
            <option value="yersinia">Yersinia</option>
            <option value="ypseudotuberculosis">Yersinia pseudotuberculosis</option>
            <option value="yruckeri">Yersinia ruckeri</option>
        </param>

        <param name="snippy_opt" argument="--snippy_opt" type="text" value="" label="Snippy options" help="Options to pass to snippy eg. '--mincov 10 --ram 32'" /> 
        <param name="roary_opt" argument="--roary_opt" type="text" value="" label="Roary options" help="Options to pass to roary eg. '-iv 1.75 -s -cd 97'" /> 
        <param name="mask" argument="--mask" type="text" value="AUTO" label="Mask regions (BED)" help="Mask core SNPS in these regions or 'auto'" /> 
        </section>

        <section name="plugins" title="Plugins">
        <param name="assembler" argument="--assembler" type="select" label="Assembler to use" help="Which assembler would you like shovill to use, default is skesa">
            <option value="skesa" selected="True">skesa</option>
            <option value="skesa_fast">skesa fast</option>
            <option value="megahit">megahit</option>
            <option value="shovill">shovill</option>
            <option value="spades">Spades</option>
        </param>
        <param name="assembler_opt" argument="--assembler_opt" type="text" value="" label="Extra assembler options to pass" help="" /> 
        <param name="treebuilder" argument="--treebuilder" type="select" label="Tree-builder to use" help="Which tree builder would you like to use, default is iqtree_fast">
            <option value="fasttree">fasttree</option>
            <option value="iqtree">iqtree</option>
            <option value="iqtree_fast" selected="True">iqtree_fast</option>
            <option value="iqtree_slow">iqtree_slow</option>
        </param>
        <param name="treebuilder_opt" argument="--treebuilder_opt" type="text" value="" label="Extra tree-builder options to pass" help="" /> 
        <param name="taxoner" argument="--taxoner" type="select" label="Species ID tool to use" help="Which taxoner would you like to use, default is kraken">
            <option value="kraken" selected="True">kraken</option>
            <option value="centrifuge">centrifuge</option>
        </param>
        <param name="taxoner_opt" argument="--taxoner_opt" type="text" value="" label="Extra taxoner options to pass" help="" /> 
        <param name="annotator" argument="--annotator" type="select" label="Genome annotator to use" help="Which genome annotator would you like to use, default is prokka_fast">
            <option value="prokka_fast" selected="True">prokka_fast</option>
        </param>
        <param name="annotator_opt" argument="--annotator_opt" type="text" value="" label="Extra annotator options to pass" help="" /> 
        </section>

     </inputs>

    <outputs>
        <data name="nullarbor_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/nullarbor.log" >
            <filter>log</filter>
        </data>
        <data name="report" format="html"  label="${tool.name} on ${on_string}: Report" from_work_dir="out/report/index.html"/>
        <data name="jobinfo" format="txt"  label="${tool.name} on ${on_string}: jobinfo.csv" from_work_dir="out/report/jobinfo.csv"/>
        <data name="seqdata" format="txt"  label="${tool.name} on ${on_string}: seqdata.csv" from_work_dir="out/report/seqdata.csv"/>
        <data name="identification" format="txt"  label="${tool.name} on ${on_string}: identification.csv" from_work_dir="out/report/identification.csv"/>
        <data name="mlst" format="tabular"  label="${tool.name} on ${on_string}: mlst.csv" from_work_dir="out/report/mlst.csv"/>
        <data name="resitome" format="tabular"  label="${tool.name} on ${on_string}: resitome.csv" from_work_dir="out/report/resitome.csv"/>
        <data name="virulome" format="tabular"  label="${tool.name} on ${on_string}: virulome.csv" from_work_dir="out/report/virulome.csv"/>
        <data name="assembly" format="txt"  label="${tool.name} on ${on_string}: assembly.csv" from_work_dir="out/report/assembly.csv"/>
        <data name="reference" format="txt"  label="${tool.name} on ${on_string}: reference.csv" from_work_dir="out/report/reference.csv"/>
        <data name="core" format="txt"  label="${tool.name} on ${on_string}: core.csv" from_work_dir="out/report/core.csv"/>
        <data name="core_newick" format="txt"  label="${tool.name} on ${on_string}: core.newick" from_work_dir="out/report/core.newick"/>
        <data name="snpdist" format="tabular"  label="${tool.name} on ${on_string}: snpdist.csv" from_work_dir="out/report/snpdist.csv"/>
        <data name="pan" format="txt"  label="${tool.name} on ${on_string}: pan.csv" from_work_dir="out/report/pan.csv"/>
    </outputs>

    <tests>
        <test>
        </test>
    </tests>
    
    <help><![CDATA[
        NAME
            nullarbor.pl 2.0.20181010
        SYNOPSIS
            Reads to reports for public health microbiology
        AUTHOR
            Torsten Seemann
        USAGE
            nullarbor.pl [options] --name NAME --ref REF.FA/GBK --input INPUT.TAB --outdir DIR
        
        DOCUMENTATION
            https://github.com/tseemann/nullarbor

    ]]></help>

    <citations>
        <citation type="bibtex">
@UNPUBLISHED{Seemann2018,
    author = {Seemann, Torsten},
    title = {Nullarbor: Pipeline to generate complete public health microbiology reports from sequenced isolates},
    year = {2018},
    url = {https://github.com/tseemann/nullarbor},
}
        </citation>
    </citations>

</tool>