comparison quast.xml @ 13:675488238c96 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"

12:875d0f36d66f

    <expand macro="bio_tools"/>
    <expand macro='requirements' />
    <command detect_errors="exit_code">
    <![CDATA[
#import re

#if str($in.custom) == 'false'
    #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $in.inputs])
    echo $labels &&
#else

    #for $read in $reads.input_1
        --pe1 '$read'
    #end for
    #for $read in $reads.input_2
        --pe2 '$read'
    #end for  
#else if $reads.reads_option == 'paired_interlaced'
    #for $read in $reads.input_1
        --pe12 '$read'
    #end for
#else if $reads.reads_option == 'mate_paired'

    #for $read in $reads.input_1
        --nanopore '$read'
    #end for
#end if

--labels $labels
-o outputdir

#if $assembly.type == 'genome'
    #if $assembly.ref.use_ref == 'true'
    -r '$assembly.ref.r'
        #if $assembly.ref.features

        -r '$assembly.ref.r'
    #else if $assembly.ref.origin == 'list'
        --references-list '$temp_ref_list_fp'
    #else if $assembly.ref.origin == 'silva'
        --test-no-ref
        --max-ref-num '$assembly.ref.max_ref_num'
    #end if
#end if

--min-contig $min_contig
$split_scaffolds

$genes.conserved_genes_finding
$alignments.use_all_alignments
--min-alignment $alignments.min_alignment
--min-identity $alignments.min_identity
--ambiguity-usage '$alignments.ambiguity_usage'
--ambiguity-score '$alignments.ambiguity_score'
$alignments.fragmented
$alignments.upper_bound_assembly
#if $alignments.upper_bound_min_con
    --upper-bound-min-con $alignments.upper_bound_min_con
#end if

&& mkdir -p '$report_html.files_path'
&& cp outputdir/*.html '$report_html.files_path'

#if ($assembly.type == 'genome' and $assembly.ref.use_ref) or ($assembly.type == 'metagenome' and $assembly.ref.origin != 'none')
    && cp -R outputdir/icarus_viewers '$report_html.files_path'
#end if

    ]]>
    </command>
    <inputs>

                <option value="mate_paired">Illumina mate-pair reads</option>
                <option value="pacbio">Pacbio SMRT reads</option>
                <option value="nanopore">Nanopore reads</option>
            </param>
            <when value="disabled"/>

            <when value="single">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
            </when>

            <when value="paired">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
                <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
            </when>

            <when value="paired_interlaced">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
            </when>

            <when value="mate_paired">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
                <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
            </when>

            <when value="pacbio">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
            </when>

            <when value="nanopore">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
            </when>
        </conditional>

        <conditional name="assembly">
            <param name="type" type="select" label="Type of assembly">
                <option value="genome">Genome</option>
                <option value="metagenome">Metagenome</option>
            </param>

            <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/>
            <param argument="--skip-unaligned-mis-contigs" type="boolean" truevalue="" falsevalue="--skip-unaligned-mis-contigs" checked="true" label="Distinguish contigs with more than 50% unaligned bases as a separate group of contigs?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/>
            <param argument="--fragmented-max-indent" type="integer" min="0" value="" optional="true" label="Fragment max indent" help="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments. The value should be less than extensive misassembly size.Default value is 50. Note: requires --fragmented option" />
        </section>
        <param name="output_files" type="select" display="checkboxes" optional="true" multiple="true" label="Output files">
            <option value="html" selected="true">HTML report</option>
            <option value="pdf">PDF report</option>
            <option value="tabular">Tabular reports</option>
            <option value="log">Log file</option>
        </param>
    </inputs>
    <outputs>
        <data name="quast_tabular" format="tabular" label="${tool.name} on ${on_string}: tabular report" from_work_dir="outputdir/report.tsv">
            <filter>'tabular' in output_files</filter>
        </data>
        <data name="report_html" format="html" label="${tool.name} on ${on_string}:  HTML report" from_work_dir="outputdir/report.html">
            <filter>'html' in output_files</filter>
        </data>
        <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}:  PDF report" from_work_dir="outputdir/report.pdf">
            <filter>'pdf' in output_files</filter>
        </data>
        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log">
            <filter>'log' in output_files</filter>
        </data>
        <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies report" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
            <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
            <filter>'tabular' in output_files</filter>
        </data>

            <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['k_mer']['k_mer_stats'] != ''</filter>
            <filter>'tabular' in output_files</filter>
        </data>
        <data name="circos_output" format="png" from_work_dir="outputdir/circos/circos.png" label="${tool.name} on ${on_string}: Circos plot">
            <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['circos']</filter>
        </data>
    </outputs>
    <tests>
        <!-- Test 01: reference, genes annotations and operon coordinates -->
        <test expect_num_outputs="2">

                </conditional>
            </conditional>
            <param name="output_files" value="html,pdf,tabular,log"/>
            <output name="report_html" file="test2_report.html" ftype="html" compare="sim_size"/>
            <output name="report_pdf" file="test2_report.pdf" ftype="pdf" compare="sim_size"/>
            <output name="quast_tabular" file="test2_report.tab" ftype="tabular"/>
            <output name="log" file="test2.log" ftype="txt" compare="sim_size"/>
            <output name="mis_ass" file="test2_missasemblies.tab" ftype="tabular"/>
            <output name="unalign" file="test2_unaligned.tab" ftype="tabular"/>
            <output name="kmers" file="test2_kmers.tab" ftype="tabular"/>
            <output name="circos_output" file="test2_circos.png" ftype="png" compare="sim_size"/>

                <param name="extensive_mis_size" value="1000"/>
                <param name="scaffold_gap_max_size" value="1000"/>
                <param name="unaligned_part_size" value="500"/>
                <param name="skip_unaligned_mis_contigs" value="-"/>
            </section>
            <param name="output_files" value="tabular"/>
            <output name="quast_tabular" file="test4.tab" ftype="tabular"/>
        </test>
        <!-- Test 05: FASTQ read files -->
        <test expect_num_outputs="3">
            <conditional name="in">
                <param name="custom" value="true"/>

            <section name="alignments">
                <param name="upper_bound_assembly" value="true"/>
                <param name="upper_bound_min_con" value="1"/>
            </section>
            <param name="output_files" value="tabular"/>
            <output name="quast_tabular" file="test5.tab" ftype="tabular"/>
            <output name="mis_ass" file="test5_missasemblies.tab" ftype="tabular"/>
            <output name="unalign" file="test5_unaligned.tab" ftype="tabular"/>
        </test>
        <!-- Test 6: FASTQ.gz read files -->
        <test expect_num_outputs="1">
            <conditional name="in">
                <param name="custom" value="true"/>
                <repeat name="inputs">
                    <param name="input" value="contigs1.fna"/>

            <conditional name="reads">
                <param name="reads_option" value="single"/>
                <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/>
            </conditional>
            <param name="output_files" value="tabular"/>
            <output name="quast_tabular" file="test6.tab" ftype="tabular"/>
        </test>
        <!-- Test 7: FASTA.gz read files -->
        <test expect_num_outputs="1">
            <conditional name="in">
                <param name="custom" value="true"/>
                <repeat name="inputs">
                    <param name="input" value="contigs1.fna"/>

            <conditional name="reads">
                <param name="reads_option" value="single"/>
                <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
            </conditional>
            <param name="output_files" value="tabular"/>
            <output name="quast_tabular" file="test7.tab" ftype="tabular"/>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page <http://quast.sourceforge.net/docs/manual.html>`_.

**Using Quast without reference**

Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs:
 
 * Quast report in HTML format
 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
 * Quast log (a file technical information about Quast tool execution)

13:675488238c96

    <expand macro="bio_tools"/>
    <expand macro='requirements' />
    <command detect_errors="exit_code">
    <![CDATA[
#import re
#import os

#if str($in.custom) == 'false'
    #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $in.inputs])
    echo $labels &&
#else

    #for $read in $reads.input_1
        --pe1 '$read'
    #end for
    #for $read in $reads.input_2
        --pe2 '$read'
    #end for
#else if $reads.reads_option == 'paired_interlaced'
    #for $read in $reads.input_1
        --pe12 '$read'
    #end for
#else if $reads.reads_option == 'mate_paired'

    #for $read in $reads.input_1
        --nanopore '$read'
    #end for
#end if

--labels '$labels'
-o 'outputdir'

#if $assembly.type == 'genome'
    #if $assembly.ref.use_ref == 'true'
    -r '$assembly.ref.r'
        #if $assembly.ref.features

        -r '$assembly.ref.r'
    #else if $assembly.ref.origin == 'list'
        --references-list '$temp_ref_list_fp'
    #else if $assembly.ref.origin == 'silva'
        --test-no-ref
        --max-ref-num $assembly.ref.max_ref_num
    #end if
#end if

--min-contig $min_contig
$split_scaffolds

$genes.conserved_genes_finding
$alignments.use_all_alignments
--min-alignment $alignments.min_alignment
--min-identity $alignments.min_identity
--ambiguity-usage '$alignments.ambiguity_usage'
--ambiguity-score $alignments.ambiguity_score
$alignments.fragmented
$alignments.upper_bound_assembly
#if $alignments.upper_bound_min_con
    --upper-bound-min-con $alignments.upper_bound_min_con
#end if

&& mkdir -p '$report_html.files_path'
&& cp outputdir/*.html '$report_html.files_path'

#if ($assembly.type == 'genome' and $assembly.ref.use_ref) or ($assembly.type == 'metagenome' and $assembly.ref.origin != 'none')
    && cp -R outputdir/icarus_viewers '$report_html.files_path'
#end if

#if $assembly.type == 'metagenome'
    && if [[ -d "outputdir/combined_reference/" ]]; then mkdir -p '$report_html_meta.files_path' && cp outputdir/combined_reference/*.html '$report_html_meta.files_path'; fi
    #if $assembly.ref.origin != 'none'
        && if [[ -d "outputdir/combined_reference/" ]]; then cp -R outputdir/combined_reference/icarus_viewers '$report_html_meta.files_path'; fi
        && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '$krona.files_path' && cp outputdir/krona_charts/*.html '$krona.files_path'; fi
    #end if
#end if

    ]]>
    </command>
    <inputs>

                <option value="mate_paired">Illumina mate-pair reads</option>
                <option value="pacbio">Pacbio SMRT reads</option>
                <option value="nanopore">Nanopore reads</option>
            </param>
            <when value="disabled"/>
            <when value="single">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
            </when>
            <when value="paired">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
                <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
            </when>

            <when value="paired_interlaced">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
            </when>
            <when value="mate_paired">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
                <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
            </when>
            <when value="pacbio">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
            </when>
            <when value="nanopore">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
            </when>
        </conditional>
        <conditional name="assembly">
            <param name="type" type="select" label="Type of assembly">
                <option value="genome">Genome</option>
                <option value="metagenome">Metagenome</option>
            </param>

            <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/>
            <param argument="--skip-unaligned-mis-contigs" type="boolean" truevalue="" falsevalue="--skip-unaligned-mis-contigs" checked="true" label="Distinguish contigs with more than 50% unaligned bases as a separate group of contigs?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/>
            <param argument="--fragmented-max-indent" type="integer" min="0" value="" optional="true" label="Fragment max indent" help="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments. The value should be less than extensive misassembly size.Default value is 50. Note: requires --fragmented option" />
        </section>
        <param name="output_files" type="select" display="checkboxes" optional="true" multiple="true" label="Output files">
            <option value="html" selected="true">HTML reports</option>
            <option value="pdf">PDF reports</option>
            <option value="tabular">Tabular reports</option>
            <option value="log">Log file</option>
            <option value="summary">Key metric summary (metagenome mode)</option>
            <option value="krona">Krona charts (metagenome mode without reference genomes)</option>
        </param>
    </inputs>
    <outputs>
        <data name="report_tabular" format="tabular" label="${tool.name} on ${on_string}: tabular report" from_work_dir="outputdir/report.tsv">
            <filter>assembly['type'] == 'genome' and 'tabular' in output_files</filter>
        </data>
        <data name="report_tabular_meta" format="tabular" label="${tool.name} on ${on_string}: tabular report for combined reference genome" from_work_dir="outputdir/combined_reference/report.tsv">
            <filter>assembly['type'] == 'metagenome' and 'tabular' in output_files</filter>
        </data>
        <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html">
            <filter>'html' in output_files</filter>
        </data>
        <data name="report_html_meta" format="html" label="${tool.name} on ${on_string}: HTML report for combined reference genome"  from_work_dir="outputdir/combined_reference/report.html">
            <filter>assembly['type'] == 'metagenome' and 'html' in output_files</filter>
        </data>
        <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}:  PDF report" from_work_dir="outputdir/report.pdf">
            <filter>assembly['type'] == 'genome' and 'pdf' in output_files</filter>
        </data>
        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log">
            <filter>assembly['type'] == 'genome' and 'log' in output_files</filter>
        </data>
        <data name="log_meta" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/metaquast.log">
            <filter>assembly['type'] == 'metagenome' and 'log' in output_files</filter>
        </data>
        <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies report" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
            <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
            <filter>'tabular' in output_files</filter>
        </data>

            <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['k_mer']['k_mer_stats'] != ''</filter>
            <filter>'tabular' in output_files</filter>
        </data>
        <data name="circos_output" format="png" from_work_dir="outputdir/circos/circos.png" label="${tool.name} on ${on_string}: Circos plot">
            <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['circos']</filter>
        </data>
        <collection name="metrics_tabular" type="list" label="${tool.name} on ${on_string}: Tabular reports for key metrics" >
            <discover_datasets pattern="(?P&lt;designation&gt;.+).tsv" directory="outputdir/summary/TSV/" format="tabular"/>
            <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
        </collection>
        <collection name="metrics_pdf" type="list" label="${tool.name} on ${on_string}: PDF reports for key metrics" >
            <discover_datasets pattern="(?P&lt;designation&gt;.+).pdf" directory="outputdir/summary/PDF/" format="pdf"/>
            <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
        </collection>
        <data name="krona" format="html" label="${tool.name} on ${on_string}:  Krona chart" from_work_dir="outputdir/krona_charts/*.html">
            <filter>assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'none' and 'krona' in output_files</filter>
        </data>
    </outputs>
    <tests>
        <!-- Test 01: reference, genes annotations and operon coordinates -->
        <test expect_num_outputs="2">

                </conditional>
            </conditional>
            <param name="output_files" value="html,pdf,tabular,log"/>
            <output name="report_html" file="test2_report.html" ftype="html" compare="sim_size"/>
            <output name="report_pdf" file="test2_report.pdf" ftype="pdf" compare="sim_size"/>
            <output name="report_tabular" file="test2_report.tab" ftype="tabular"/>
            <output name="log" file="test2.log" ftype="txt" compare="sim_size"/>
            <output name="mis_ass" file="test2_missasemblies.tab" ftype="tabular"/>
            <output name="unalign" file="test2_unaligned.tab" ftype="tabular"/>
            <output name="kmers" file="test2_kmers.tab" ftype="tabular"/>
            <output name="circos_output" file="test2_circos.png" ftype="png" compare="sim_size"/>

                <param name="extensive_mis_size" value="1000"/>
                <param name="scaffold_gap_max_size" value="1000"/>
                <param name="unaligned_part_size" value="500"/>
                <param name="skip_unaligned_mis_contigs" value="-"/>
            </section>
            <param name="output_files" value="log"/>
            <output name="log_meta" ftype="txt">
			    <assert_contents>
                    <has_text text="Reference genomes are not found" />
                </assert_contents>
            </output>
        </test>
        <!-- Test 05: FASTQ read files -->
        <test expect_num_outputs="3">
            <conditional name="in">
                <param name="custom" value="true"/>

            <section name="alignments">
                <param name="upper_bound_assembly" value="true"/>
                <param name="upper_bound_min_con" value="1"/>
            </section>
            <param name="output_files" value="tabular"/>
            <output name="report_tabular" file="test5.tab" ftype="tabular"/>
            <output name="mis_ass" file="test5_missasemblies.tab" ftype="tabular"/>
            <output name="unalign" file="test5_unaligned.tab" ftype="tabular"/>
        </test>
        <!-- Test 06: FASTQ.gz read files -->
        <test expect_num_outputs="1">
            <conditional name="in">
                <param name="custom" value="true"/>
                <repeat name="inputs">
                    <param name="input" value="contigs1.fna"/>

            <conditional name="reads">
                <param name="reads_option" value="single"/>
                <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/>
            </conditional>
            <param name="output_files" value="tabular"/>
            <output name="report_tabular" file="test6.tab" ftype="tabular"/>
        </test>
        <!-- Test 07: FASTA.gz read files -->
        <test expect_num_outputs="1">
            <conditional name="in">
                <param name="custom" value="true"/>
                <repeat name="inputs">
                    <param name="input" value="contigs1.fna"/>

            <conditional name="reads">
                <param name="reads_option" value="single"/>
                <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
            </conditional>
            <param name="output_files" value="tabular"/>
            <output name="report_tabular" file="test7.tab" ftype="tabular"/>
        </test>
        <!-- Test 08: metagenomics all tab outputs-->
        <test expect_num_outputs="3">
            <conditional name="in">
                <param name="custom" value="false"/>
                <param name="inputs" value="test8.fasta"/>
            </conditional>
            <conditional name="assembly">
                <param name="type" value="metagenome"/>
                <conditional name="ref">
                    <param name="origin" value="none"/>
                </conditional>
            </conditional>
            <param name="min_contig" value="500"/>
            <param name="split_scaffolds" value="false"/>
            <param name="large" value="false"/>
            <section name="genes">
                <conditional name="gene_finding">
                    <param name="tool" value="none"/>
                </conditional>
                <param name="rna_finding" value="false"/>
                <param name="conserved_genes_finding" value="false"/>
            </section>
            <section name="alignments">
                <param name="use_all_alignments" value="false"/>
                <param name="min_alignment" value="65"/>
                <param name="min_identity" value="95.0"/>
                <param name="ambiguity_usage" value="one"/>
                <param name="ambiguity_score" value="0.99"/>
                <param name="fragmented" value="false"/>
            </section>
            <section name="advanced">
                <param name="contig_thresholds" value="0,1000"/>
                <param name="strict_NA" value="false"/>
                <param name="extensive_mis_size" value="1000"/>
                <param name="scaffold_gap_max_size" value="1000"/>
                <param name="unaligned_part_size" value="500"/>
                <param name="skip_unaligned_mis_contigs" value="-"/>
            </section>
            <param name="output_files" value="tabular,summary"/>
            <output name="report_tabular_meta" ftype="tabular">
                <assert_contents>
                    <has_text text="contigs (>= 0 bp)" />
                </assert_contents>
            </output>
            <output_collection name="metrics_tabular" type="list" count="14"/>
            <output_collection name="metrics_pdf" type="list" count="15"/>
        </test>
        <!-- Test 09: metagenomics log, html and krona outputs-->
        <test expect_num_outputs="4">
            <conditional name="in">
                <param name="custom" value="false"/>
                <param name="inputs" value="test8.fasta"/>
            </conditional>
            <conditional name="assembly">
                <param name="type" value="metagenome"/>
                <conditional name="ref">
                    <param name="origin" value="none"/>
                </conditional>
            </conditional>
            <param name="min_contig" value="500"/>
            <param name="split_scaffolds" value="false"/>
            <param name="large" value="false"/>
            <section name="genes">
                <conditional name="gene_finding">
                    <param name="tool" value="none"/>
                </conditional>
                <param name="rna_finding" value="false"/>
                <param name="conserved_genes_finding" value="false"/>
            </section>
            <section name="alignments">
                <param name="use_all_alignments" value="false"/>
                <param name="min_alignment" value="65"/>
                <param name="min_identity" value="95.0"/>
                <param name="ambiguity_usage" value="all"/>
                <param name="ambiguity_score" value="0.99"/>
                <param name="fragmented" value="false"/>
            </section>
            <section name="advanced">
                <param name="contig_thresholds" value="0,1000"/>
                <param name="strict_NA" value="false"/>
                <param name="extensive_mis_size" value="1000"/>
                <param name="scaffold_gap_max_size" value="1000"/>
                <param name="unaligned_part_size" value="500"/>
                <param name="skip_unaligned_mis_contigs" value="-"/>
            </section>
            <param name="output_files" value="html,log,krona"/>
            <output name="report_html" ftype="html">
                <assert_contents>
                    <has_text text="Vibrio_parahaemolyticus" />
                </assert_contents>
            </output>
			<output name="report_html_meta" ftype="html">
                <assert_contents>
                    <has_text text="Total length (>= 1000 bp)" />
                </assert_contents>
            </output>
			<output name="log_meta" ftype="txt">
                <assert_contents>
                    <has_text text="Vibrio_parahaemolyticus | successfully downloaded" />
                </assert_contents>
            </output>
            <output name="krona"  ftype="html">
                <assert_contents>
                    <has_text text="Vibrio_parahaemolyticus" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page <http://quast.sourceforge.net/docs/manual.html>`_.

**Using Quast without reference**

Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs:

 * Quast report in HTML format
 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
 * Quast log (a file technical information about Quast tool execution)