Mercurial > repos > iuc > quast
diff quast.xml @ 5:81df4950d65b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
author | iuc |
---|---|
date | Tue, 04 Dec 2018 06:49:05 -0500 |
parents | 0834c823d4b9 |
children | f30d03867854 |
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--- a/quast.xml Mon Feb 12 09:05:20 2018 -0500 +++ b/quast.xml Tue Dec 04 06:49:05 2018 -0500 @@ -1,60 +1,46 @@ -<tool id="quast" name="Quast" version="4.6.3" > +<tool id="quast" name="Quast" version="5.0.2" > <description>Genome assembly Quality</description> <requirements> - <requirement type="package" version="4.6.3">quast</requirement> + <requirement type="package" version="5.0.2">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> + <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 - #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 ]) +#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: - $k - #end for - && - mv outputdir/report.tsv '$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 '$log_txt' +'$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> @@ -65,6 +51,7 @@ </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" @@ -80,20 +67,16 @@ 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"> + <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="html" name="contig_size_viewer" label="Quast: Contig view"/> - <data format="html" name="alignment_viewer" label="Quast: Alignment view"> + <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)"/> - <data format="html" name="report_html" label="Quast: Report (HTML)"/> - <data format="pdf" name="report_pdf" label="Quast: Report (PDF)"/> + <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> @@ -103,6 +86,7 @@ <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> @@ -110,6 +94,8 @@ <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>