| Previous changeset 3:fb3683870b74 (2019-12-30) |
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Commit message:
"planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 6615f6e5ae2eac1f8e90f25e1707c8b7ab161517" |
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modified:
ectyper.xml |
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| diff -r fb3683870b74 -r 08d801182fa1 ectyper.xml --- a/ectyper.xml Mon Dec 30 10:10:44 2019 -0500 +++ b/ectyper.xml Fri May 29 13:09:54 2020 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="ectyper" name="ectyper" version="0.9.1"> +<tool id="ectyper" name="ectyper" version="1.0.0"> <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description> <requirements> - <requirement type="package" version="0.9.1">ectyper</requirement> + <requirement type="package" version="1.0.0">ectyper</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ @@ -20,42 +20,60 @@ #set $genomes = $input.element_identifier #end if - #if $mash_input - ln -s "${mash_input}" mash_sketch.msh && + #if $adv_param.mash_input + ln -s "${adv_param.mash_input}" mash_sketch.msh && #end if + + #if $adv_param.db_input + ln -s "${adv_param.db_input}" custom_db.json && + #end if + + ectyper --cores \${GALAXY_SLOTS:-4} --input "${genomes}" - --percentIdentity '$adv_param.min_percentIdentity' - --percentLength '$adv_param.percentLength' + -opid '$adv_param.opid' + -opcov '$adv_param.opcov' + -hpid '$adv_param.hpid' + -hpcov '$adv_param.hpcov' + #if $adv_param.verifyEcoli --verify #end if - #if $mash_input + + #if $adv_param.mash_input --refseq mash_sketch.msh - #end if - #if $adv_param.alleleSequence - --sequence #end if + + #if $adv_param.db_input + --dbpath custom_db.json + #end if + --output '.' ]]> </command> <inputs> <param name="input" type="data" format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s)"/> - <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide custom MASH genome sketch to help with species identification (otherwise default RefSeq sketch is used)"/> <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="10" min="1" max="100"/> + <param name="opid" label="O antigen minimum %identity" type="integer" value="90" min="1" max="100"/> + <param name="opcov" label="O antigen minimum %coverage" type="integer" value="90" min="1" max="100"/> + <param name="hpid" label="H antigen minimum %identity" type="integer" value="95" min="1" max="100"/> + <param name="hpcov" label="H antigen minimum %coverage" 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="blastresults" type="boolean" checked="false" label="Include BLAST allele alignment results tab-delim file in the outputs?" /> <param name="logging" type="boolean" checked="false" label="Include log file in the run outputs?" /> - </section> + <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide custom MASH genome sketch to help with species identification (otherwise default RefSeq sketch is used)"/> + <param name="db_input" type="data" optional="true" format="json" label="Custom database of alleles (Optional)" help="Optionally provide custom database of alleles in JSON format"/> + </section> </inputs> <outputs> <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report on ${input.element_identifier}"> </data> <data name="output_log" format="txt" from_work_dir="ectyper.log" label="${tool.name} log file on ${input.element_identifier}"> <filter>adv_param['logging']==True</filter> - </data> + </data> + <data name="output_blast" format="tabular" from_work_dir="blast_output_alleles.txt" label="${tool.name} BLAST results file on ${input.element_identifier}"> + <filter>adv_param['blastresults']==True</filter> + </data> </outputs> <tests> <test> @@ -76,35 +94,34 @@ **Syntax** -This tool identifies the serotype of assembled or assembly-free Escherichia coli genome sample based on a set of either *wzm/wzt* or *wzx/wzy* and *fliC/flkA/flmA* alleles corresponding to O and H antigens, respectively. -The non-E.coli genomes and other Escherichia genus species are successfully identified and well handled. The 0.9.0 version improves tool sensitivy when target alleles are truncated or -poorly covered by raw reads. +This tool identifies the serotype of both assembled or assembly-free Escherichia coli genome samples based on a set of the key O and H antigen determinant genes including *wzm/wzt* or *wzx/wzy* and *fliC/flkA/flmA*. +Unique to the tool, species identification module allows for non-E.coli genomes identification including other Escherichia genus species. +This version improves antigen call rates on "difficult samples" by use of an adaptive threshold. This is especially useful when antigen genes are truncated or poorly covered by raw reads. +If no antigen call is being predicted by the tool, try to lower %coverage parameter first. For more information on the new Quality Control module and running parameter details please visit https://github.com/phac-nml/ecoli_serotyping. -For more information please visit https://github.com/phac-nml/ecoli_serotyping. - ----- **Input:** Accepts a variety of inputs including both single and/or multiple FASTQ and/or FASTA file(s). Inputs might contain pure raw reads, but for more accurate results, draft assemblies are recommended. -The default MASH RefSeq genome sketch is included and updated every 6 months, but one can supply custom sketch file for species identification. -One can download RefSeq genome sketch containing approximately 91,283 genomes from https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh. +The default MASH RefSeq genome sketch (https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh) containing approximately 91K genomes is included and automatically updated every 6 months. + **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 +Tab-delimited report listing identified O and H antigens together with corresponding the highest-scoring alleles and normalized BLAST score defined as (%identity x %coverage) / 1e4. +If *verifyEcoli* parameter is enabled, final report will contain allele quality control information on results for reporting purposes. PASS (REPORTABLE) QC flag means that O and H antigen calls are of sufficient to unambiguously resolve them from all other antigens. ----- **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 + - **Enable E. coli species verification:** for species verification in case samples are of non-E.coli origin + - **Include BLAST allele alignment results tab-delim file in the outputs?** Get reference allele sequences and detailed BLAST output + - **Include log file in the run outputs?:** Get optional logs of the ectyper run for a more detailed results assessment and troubleshooting </help> <citations> |