Mercurial > repos > nml > ectyper
view ectyper.xml @ 1:b02c775b27c8 draft
planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
author | nml |
---|---|
date | Thu, 31 Jan 2019 09:39:04 -0500 |
parents | b60c187a3a02 |
children | e79a8dad83b4 |
line wrap: on
line source
<tool id="ectyper" name="ectyper" version="0.8.1"> <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description> <requirements> <requirement type="package" version="0.8.1">ectyper</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ #set $genomes = '' #if hasattr($input, '__iter__') #for $i in $input ln -s "${i}" "${i.name}" && #if len($genomes) > 0 #set $genomes = $genomes + ',' + str($i.name) #else #set $genomes = str($i.name) #end if #end for #else ln -s "${input}" "${input.name}" && #set $genomes = $input.name #end if #if $mash_input ln -s "${mash_input}" mash_sketch.msh && #end if ectyper --cores \${GALAXY_SLOTS:-4} --input "${genomes}" --percentIdentity '$adv_param.min_percentIdentity' --percentLength '$adv_param.percentLength' #if $adv_param.verifyEcoli --verify #end if #if $mash_input --refseq mash_sketch.msh #end if #if $adv_param.alleleSequence --sequence #end if --output '.' ]]> </command> <inputs> <param name="input" type="data" format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s) with contig(s)"/> <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide MASH sketches to find closest genome (in case O/H typing fails)"/> <section name="adv_param" title="Advanced parameters" expanded="False"> <param name="min_percentIdentity" type="integer" value="90" min="1" max="100"/> <param name="percentLength" type="integer" value="50" min="1" max="100"/> <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/> <param name="alleleSequence" type="boolean" checked="false" label="Print the allele sequences as the final columns of the output?"/> <param name="logging" type="boolean" checked="false" label="Include log file in the run outputs?" /> </section> </inputs> <outputs> <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report"> </data> <data name="output_log" format="text" from_work_dir="ectyper.log" label="${tool.name} log file"> <filter>adv_param['logging']==True</filter> </data> </outputs> <tests> <test> <param name="input" value="Escherichia2.fastq"/> <assert_stderr> <has_text text="O22"/> <has_text text="H8"/> </assert_stderr> <output name="output_result" ftype="tabular" > <assert_contents> <has_text_matching expression="O22"/> </assert_contents> </output> </test> </tests> <help> **Syntax** This tool identifies the serotype of Escherichia coli genome sequences based on a set of *wzm/wzt*, *wzx/wzy* and *fliC/flkA/flmA* alleles corresponding to O and H antigens, respectively. For more information please visit https://github.com/phac-nml/ecoli_serotyping. ----- **Input:** Accepts a variety of inputs including single or multiple FASTQ and/or FASTA file(s). Inputs might contain pure raw reads, but for more accurate results draft assemblies are recommended. Optionally select a MASH RefSeq genome sketch (version 2.0 and above) for cases when O/H typing would fail. Download RefSeq genome sketch containing 91,283 genomes with 1000 hashes each directly from https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh . **Output:** Tab-delimited report listing identified O and H antigens together with corresponding highest scoring alleles and normalized BLAST score defined as (%identity x query coverage length) / 10000 ----- **Parameters (Optional):** - **Print the allele sequences as the final columns of the output?** Turn ON/OFF addition of the actual O and H antigen allelic sequences in the report - **Enable E. coli species verification:** Turn ON/OFF for more rigorous species verification (recommended) - **Include log file in the run outputs?:** Turn ON/OFF optional output of the ectyper log file for a more detailed results assessment </help> <citations> <citation type="bibtex"> @misc{githubectyper, author = {Laing Chad}, title = {ECtyper - serotyping module for Escherichia coli}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/phac-nml/ecoli_serotyping} }</citation> </citations> </tool>