comparison quast.xml @ 5:81df4950d65b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa

4:0834c823d4b9

<tool id="quast" name="Quast" version="4.6.3" >
    <description>Genome assembly Quality</description>
    <requirements>
        <requirement type="package" version="4.6.3">quast</requirement>
    </requirements>
    <stdio>
        <regex match="ERROR! exception caught!"
            source="both"
            level="fatal"
            description="Something went wrong. Check the following errors : No labels..." />
    </stdio>
    <command>
    <![CDATA[
        #import re
        quast
        --threads \${GALAXY_SLOTS:-4}
        -o outputdir
        #if $gene_selection == "eukaryote":
            --eukaryote
        #else if $gene_selection == "metagenes":
            --meta
        #end if
        #if $input_ref:
            -R '$input_ref'
            #if $input_operon:
                -O '$input_operon'
            #end if
            #if $annot:
                -G '$annot'
            #end if
        #end if
        #if $input_size:
            --est-ref-size $input_size
        #end if
        --min-contig $min_contig
        -l
        #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.element_identifier))+'"' for $x in $input ])

        $names
        --contig-thresholds $threshold_contig
        #for $k in $input:
            $k 
        #end for
        &&
        mv outputdir/report.tsv '$quast_tsv' &&
        ## The sed string below removes non-functional "Main menu" button from the viewer
        sed '\:<div class="btn btn-inverse" id="to_main_menu_button">:,\:</div>:d' outputdir/icarus_viewers/contig_size_viewer.html > '$contig_size_viewer' &&
        #if $input_ref:
            ## The sed string below removes non-functional "Main menu" button from the viewer
            sed '\:<div class="btn btn-inverse" id="to_main_menu_button">:,\:</div>:d' outputdir/icarus_viewers/alignment_viewer.html > '$alignment_viewer' &&
        #end if
        ## The sed string below removes non-functional link from the report page
        sed "\:<div id='icarus-json'>:,\:</div>:d" outputdir/report.html > '$report_html' &&
        mv outputdir/report.pdf '$report_pdf' &&
        mv outputdir/contigs_reports/misassemblies_report.tsv '$mis_ass_tsv' &&
        mv outputdir/contigs_reports/unaligned_report.tsv '$unalign_tsv' &&
        mv outputdir/quast.log '$log_txt'
    ]]>
    </command>
    <inputs>
        <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file" multiple="True"/>
        <param name="type_file" type="select" label="Type of data">
            <option value="contig">Contig</option>
            <option value="scaffold">Scaffold</option>
        </param>
        <param name="input_size" type="integer" label="Size of reference genome" optional="True"  argument="--est-ref-size"
            help="Estimated reference genome size (in bp) for computing NGx statistics, if known. This value will be used only if a reference genome file is not specified "/>
        <param name="input_ref" type="data" format="fasta" label="Reference genome" optional="True"  argument="-R"
            help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."/>
        <param name="annot" type="data" format="gff, gff3, bed" label="Gene Annotations" optional="True" argument="-G"
            help="Gene coordinates for the reference genome (only relevant if the reference genome is used). "/>
        <param name="input_operon" type="data" format="gff, gff3, bed" label="Operon Annotations"  optional="True" argument="-O" help="Operon coordinates for the reference genome (only relevant if the reference genome is used)."/>

            help="Set the lower threshold for a contig length. Shorter contigs won't be taken into account [default is 500]"/>
        <param name="threshold_contig" type="text" value="0,1000" label="Thresholds" argument="--contig-thresholds"
            help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.[default is 0,1000]"/>
    </inputs>
    <outputs>
        <data format="txt" name="log_txt" label="Quast: Log" />
        <data format="tabular" name="mis_ass_tsv" label="Quast: Misassemblies">
            <filter>input_ref is not None</filter>
        </data>
        <data format="tabular" name="unalign_tsv" label="Quast: Unaligned contigs">
            <filter>input_ref is not None</filter>
        </data>
        <data format="html" name="contig_size_viewer" label="Quast: Contig view"/>
        <data format="html" name="alignment_viewer" label="Quast: Alignment view">
            <filter>input_ref is not None</filter>
        </data>
        <data format="tabular" name="quast_tsv" label="Quast: Report (tabulal)"/>
        <data format="html" name="report_html" label="Quast: Report (HTML)"/>
        <data format="pdf" name="report_pdf" label="Quast: Report (PDF)"/>
    </outputs>
    <tests>
        <test>
            <!-- Test with reference and genes annotations -->
            <param name="input" value="contigs2.fna,contigs1.fna"/>
            <param name="input_ref" value="reference.fna"/>
            <param name="type_file" value="contig"/>
            <param name="annot" value="genes.gff"/>
            <param name="gene_selection" value="prokaryotes"/>
            <output name="quast_tsv" file="test1_output.tsv" lines_diff="4"/>
        </test>
        <test>
            <!-- Test without reference -->
            <param name="input" value="contigs2.fna,contigs1.fna"/>
            <param name="type_file" value="contig"/>
            <output name="quast_tsv" file="test2_output.tsv" lines_diff="4"/>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

5:81df4950d65b

<tool id="quast" name="Quast" version="5.0.2" >
    <description>Genome assembly Quality</description>
    <requirements>
        <requirement type="package" version="5.0.2">quast</requirement>
    </requirements>
    <command detect_errors="exit_code">
    <![CDATA[
#import re
quast
--threads \${GALAXY_SLOTS:-4}
-o outputdir
#if $gene_selection == "eukaryote":
    --eukaryote
#else if $gene_selection == "metagenes":
    --meta
#end if
$large
#if $input_ref:
    -R '$input_ref'
    #if $input_operon:
        -O '$input_operon'
    #end if
    #if $annot:
        -g '$annot'
    #end if
#end if
#if $input_size:
    --est-ref-size $input_size
#end if
--min-contig $min_contig
-l
#set names = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $input ])

'$names'
--contig-thresholds $threshold_contig
#for $k in $input:
    $k 
#end for
&& mkdir '$report_html.files_path'
&& cp outputdir/*.html '$report_html.files_path'
#if str($input_ref):
    && cp -R outputdir/icarus_viewers '$report_html.files_path'
#end if
    ]]>
    </command>
    <inputs>
        <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file" multiple="True"/>
        <param name="type_file" type="select" label="Type of data">
            <option value="contig">Contig</option>
            <option value="scaffold">Scaffold</option>
        </param>
        <param name="input_size" type="integer" label="Size of reference genome" optional="True"  argument="--est-ref-size"
            help="Estimated reference genome size (in bp) for computing NGx statistics, if known. This value will be used only if a reference genome file is not specified "/>
        <param argument="--large" type="boolean" truevalue="--large" falsevalue="" label="Run quast in --large mode for large genomes" help="Uses minimap2 aligner, improves transposable element handling and alignment thresholds"/>
        <param name="input_ref" type="data" format="fasta" label="Reference genome" optional="True"  argument="-R"
            help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."/>
        <param name="annot" type="data" format="gff, gff3, bed" label="Gene Annotations" optional="True" argument="-G"
            help="Gene coordinates for the reference genome (only relevant if the reference genome is used). "/>
        <param name="input_operon" type="data" format="gff, gff3, bed" label="Operon Annotations"  optional="True" argument="-O" help="Operon coordinates for the reference genome (only relevant if the reference genome is used)."/>

            help="Set the lower threshold for a contig length. Shorter contigs won't be taken into account [default is 500]"/>
        <param name="threshold_contig" type="text" value="0,1000" label="Thresholds" argument="--contig-thresholds"
            help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.[default is 0,1000]"/>
    </inputs>
    <outputs>
        <data format="txt" name="log_txt" label="Quast: Log" from_work_dir="outputdir/quast.log"/>
        <data format="tabular" name="mis_ass_tsv" label="Quast: Misassemblies" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
            <filter>input_ref is not None</filter>
        </data>
        <data format="tabular" name="unalign_tsv" label="Quast: Unaligned contigs" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv">
            <filter>input_ref is not None</filter>
        </data>
        <data format="tabular" name="quast_tsv" label="Quast: Report (tabulal)" from_work_dir="outputdir/report.tsv"/>
        <data format="html" name="report_html" label="Quast: Report (HTML)" from_work_dir="outputdir/report.html"/>
        <data format="pdf" name="report_pdf" label="Quast: Report (PDF)" from_work_dir="outputdir/report.pdf"/>
    </outputs>
    <tests>
        <test>
            <!-- Test with reference and genes annotations -->
            <param name="input" value="contigs2.fna,contigs1.fna"/>
            <param name="input_ref" value="reference.fna"/>
            <param name="type_file" value="contig"/>
            <param name="annot" value="genes.gff"/>
            <param name="gene_selection" value="prokaryotes"/>
            <param name="large" value="true"/>
            <output name="quast_tsv" file="test1_output.tsv" lines_diff="4"/>
        </test>
        <test>
            <!-- Test without reference -->
            <param name="input" value="contigs2.fna,contigs1.fna"/>
            <param name="type_file" value="contig"/>
            <output name="quast_tsv" file="test2_output.tsv" lines_diff="4"/>
            <output name="report_html" file="test2_report.html" lines_diff="50"/>
            <output name="report_pdf" file="test2_report.pdf" compare="sim_size"/>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**