Mercurial > repos > iuc > quast
diff quast.xml @ 0:736d51130b41 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
author | iuc |
---|---|
date | Tue, 13 Sep 2016 14:43:54 -0400 |
parents | |
children | 0edbf19cf5eb |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/quast.xml Tue Sep 13 14:43:54 2016 -0400 @@ -0,0 +1,129 @@ +<tool id="quast" name="Quast" version="4.1" > + <description>Genome assembly Quality</description> + <requirements> + <requirement type="package" version="4.1">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[ + quast + -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 + --contig-thresholds $threshold_contig + #for $k in $files: + #if $k.type_file == "scaffold": + -s + #end if + $k.input + #end for + && + mv outputdir/report.txt '$quast_out' && + mv outputdir/report.tsv '$quast_tsv' && + mv outputdir/report.tex '$quast_tex' && + mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' && + mv outputdir/report.html '$report_html' + ]]> + </command> + <inputs> + <repeat name="files" title="Input assembly files" min="1"> + <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file"/> + <param name="type_file" type="select" label="Type of data"> + <option value="contig">Contig</option> + <option value="scaffold">Scaffold</option> + </param> + </repeat> + <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 File" 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="txt" label="Gene Annotations" optional="True" argument="-G" + help="File with gene positions in the reference genome. "/> + <param name="input_operon" type="data" format="txt" label="Operon Annotations" optional="True" argument="-O" + help="File with operon positions in the reference genome"/> + <param name="gene_selection" type="select" label="Type of organism"> + <option value="prokaryotes">Prokaryotes</option> + <option value="eukaryote">Eukaryote</option> + <option value="metagenes">Metagenomes</option> + </param> + <param name="min_contig" type="integer" value="500" label="Lower Threshold" argument="--min-contig" + 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="quast_out" label="Quast report.txt" from_work_dir="Quast_report.txt"/> + <data format="tsv" name="quast_tsv" label="Quast report.tsv" from_work_dir="Quast_report.tsv"/> + <data format="tex" name="quast_tex" label="Quast report.tex" from_work_dir="Quast_report.tex"/> + <data format="html" name="icarus" label="Icarus Contig size viewer" from_work_dir="Icarus.html"/> + <data format="html" name="report_html" label="Quast report.html" from_work_dir="Quast_report.html"/> + </outputs> + <tests> + <test> + <param name="input" value="contigs_1.fasta"/> + <param name="input.type_file" value="contig"/> + <param name="gene_selection" value="prokaryotes"/> + <output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/> + </test> + </tests> + <help> +<![CDATA[ +**Description** + +Galaxy tool wrapper for the QUAST tool. Quast stands for QUality ASsessment Tool. It evaluates genome assemblies by computing various metrics. + +----- + +**Inputs and Outputs** + +- Input: + + The tool accepts assemblies and references in FASTA format. + + The tool accepts annotation and operon files in: + + GFF, versions 2 and 3 (note: feature/type field should be either "gene" or "operon") + + the format used by NCBI for genes ("Summary (text)"); + + four tab-separated columns: sequence name, gene/operon id, start position, end position + +- Output: + + An assessment summary in plain text format + + An assessment summary in tabulation separated values format + + An assessment summary in LateX format + + An assessment summary in HTML format + + An HTML view of contig sizes wit Icarus + + + ]]> + </help> + + <citations> + <citation type="bibtex">@ARTICLE{a1, + author = {Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler}, + title = {QUAST: quality assessment tool for genomce assemblies, Bioinformatics (2013) 29 (8): 1072-1075} + }</citation> + <citation type="bibtex">@misc{quast41, + title = {{Quast} v4.1}, + howpublished = {http://bioinf.spbau.ru/quast}, + note = {Released May 2016}} + }</citation> + </citations> +</tool>