Mercurial > repos > iss > chewbbaca
diff chewbbaca.xml @ 0:a3b5bee8ae1b draft
Uploaded
| author | iss |
|---|---|
| date | Fri, 03 May 2019 10:06:09 -0400 |
| parents | |
| children | 872ed5ee7b98 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chewbbaca.xml Fri May 03 10:06:09 2019 -0400 @@ -0,0 +1,305 @@ +<tool id="chewBBACA" name="chewBBACA" version="2.0"> + <description>BSR-Based Allele Calling Algorithm + </description> + <requirements> + <requirement type="package" version="3.6">Python</requirement> + <requirement type="package" version="1.15.3">numpy</requirement> + <requirement type="package" version="0.19.1">scipy</requirement> + <requirement type="package" version="5.22.2.1">perl</requirement> + <requirement type="package" version="1.72">biopython</requirement> + <requirement type="package" version="3.8.1">plotly</requirement> + <requirement type="package" version="1.8.2">SPARQLWrapper</requirement> + <requirement type="package" version="0.23.4">pandas</requirement> + <requirement type="package" version="2.5.0">blast</requirement> + <requirement type="package" version="2.6.3">prodigal</requirement> + <requirement type="package" version="2.1">clustalw</requirement> + <requirement type="package" version="7.313">mafft</requirement> + <requirement type="package" version="2.0.16">chewbbaca</requirement> + </requirements> + <!-- basic error handling --> + <stdio> + <!-- Assume anything other than zero is an error --> + <exit_code range="1:" level="fatal" description="Tool exception" /> + <exit_code range=":-1" level="fatal" description="Tool exception" /> + </stdio> + <command> + perl + $__tool_directory__/chewBBACA.pl $selectFunction.myFunctions + #if str( $selectFunction.myFunctions ) in ('CreateSchema', 'AlleleCall') + '${",".join(map(str, $selectFunction.input1))}' + #elif str( $selectFunction.myFunctions ) in ('SchemaEvaluator', 'TestGenomeQuality', 'ExtractCgMLST', 'RemoveGenes') + $selectFunction.input1 + #else + 'NULL' + #end if + #if str( $selectFunction.myFunctions ) == 'AlleleCall' + #set $input_names = [] + #for $input in $selectFunction.input1 + $input_names.append($input.element_identifier) + #end for + #set $input_name = ",".join(map(str, $input_names)) + '$input_name' + #else + 'NULL' + #end if + #if str( $selectFunction.myFunctions ) == 'CreateSchema' + '$schema' + #elif str( $selectFunction.myFunctions ) == 'AlleleCall' + '$statistics,$contigsinfo,$alleles,$logginginfo,$repeatedloci' + #elif str( $selectFunction.myFunctions ) == 'SchemaEvaluator' + '$schemaplot' + #elif str( $selectFunction.myFunctions ) == 'TestGenomeQuality' + '$thresholdplot,$removedgenomes' + #elif str( $selectFunction.myFunctions ) == 'RemoveGenes' + '$removedgenes' + #else + 'NULL' + #end if + + "chewBBACA.py $selectFunction.myFunctions + #if str( $selectFunction.myFunctions ) in ('CreateSchema', 'AlleleCall', 'TestGenomeQuality', 'ExtractCgMLST') + -o output_dir + #end if + #if str( $selectFunction.myFunctions ) == 'RemoveGenes' + -o output_removegenes + #end if + #if str( $selectFunction.myFunctions ) in ('CreateSchema', 'AlleleCall') + -i input_dir + --cpu \${GALAXY_SLOTS:-4} + #end if + #if str( $selectFunction.myFunctions ) in ('SchemaEvaluator', 'TestGenomeQuality', 'ExtractCgMLST', 'RemoveGenes') + -i $selectFunction.input1 + #end if + #if str( $selectFunction.myFunctions ) in ('CreateSchema', 'AlleleCall') + #if $selectFunction.bsr + --bsr $selectFunction.bsr + #end if + + #if $selectFunction.ptfmode.ptf_select=="system" + --ptf ${ filter( lambda x: str( x[0] ) == str( $selectFunction.ptfmode.ptf_system ), $__app__.tool_data_tables[ 'chewbbaca_ptfs' ].get_fields() )[0][-1] } + #elif $selectFunction.ptfmode.ptf_select=="user" + --ptf $selectFunction.ptfmode.ptf_user + #end if + #end if + #if str( $selectFunction.myFunctions ) == 'CreateSchema' + #if $selectFunction.minBpLocus + -l $selectFunction.minBpLocus + #end if + #end if + #if str( $selectFunction.myFunctions ) == 'AlleleCall' + #if $selectFunction.mode.schema_select=="system" + -g ${ filter( lambda x: str( x[0] ) == str( $selectFunction.mode.reference ), $__app__.tool_data_tables[ 'chewbbaca_schemas' ].get_fields() )[0][-1] } + #else + -g $selectFunction.mode.genes + #end if + #end if + #if str( $selectFunction.myFunctions ) == 'SchemaEvaluator' + --cpu \${GALAXY_SLOTS:-4} + #if $selectFunction.conserved + -p + #end if + -l output_rms/SchemaEvaluator.html + -ta $selectFunction.ncbiTA + -t $selectFunction.threshold + #if $selectFunction.title + --title '$selectFunction.title' + #end if + -s $selectFunction.numBoxplots + #if $selectFunction.light + --light + #end if + #end if + #if str( $selectFunction.myFunctions ) == 'TestGenomeQuality' + -n $selectFunction.maxNumIterations + -t $selectFunction.maxThreshold + -s $selectFunction.stepThreshold + #end if + #if str( $selectFunction.myFunctions ) == 'ExtractCgMLST' + #if $selectFunction.genes + -r $selectFunction.genes + #end if + #if $selectFunction.genomes + -g $selectFunction.genomes + #end if + #if $selectFunction.maxPresence + -p $selectFunction.maxPresence + #end if + #end if + #if str( $selectFunction.myFunctions ) == 'RemoveGenes' + -g $selectFunction.genes + #end if + " + </command> + + <inputs> + <conditional name="selectFunction"> + <param name="myFunctions" type="select" label="Select function"> + <option value="CreateSchema">CreateSchema: Create a gene by gene schema based on genomes</option> + <option value="AlleleCall" selected="true">AlleleCall: Perform allele call for target genomes</option> + <option value="SchemaEvaluator">SchemaEvaluator: Tool that builds an html output to better navigate/visualize your schema</option> + <option value="TestGenomeQuality">TestGenomeQuality: Analyze your allele call output to refine schemas</option> + <option value="ExtractCgMLST">ExtractCgMLST: Select a subset of loci without missing data (to be used as PHYLOViZ input)</option> + <option value="RemoveGenes">RemoveGenes: Remove a provided list of loci from your allele call output</option> + </param> + <when value="CreateSchema"> + <param name="input1" format="fasta" type="data" multiple="true" label="Selection of genome files (fasta)" /> + <param name="bsr" type="text" value="0.6" optional="true" label="minimum BSR score" /> + <conditional name="ptfmode"> + <param name="ptf_select" type="select" display="radio" label="Which Prodigal training file would you like to use?"> + <option value="system" selected="True">System training file</option> + <option value="user">Own training file</option> + </param> + <when value="system"> + <param name="ptf_system" type="select" label="Choose Prodigal training file"> + <options from_data_table="chewbbaca_ptfs" /> + </param> + </when> + <when value="user"> + <param name="ptf_user" format="binary" type="data" optional="true" multiple="false" label="Prodigal Training File" /> + </when> + </conditional> + <param name="minBpLocus" type="integer" value="200" optional="true" label="minimum bp locus lenght" help="Integer" /> + </when> + <when value="AlleleCall"> + <param name="input1" format="fasta" type="data" multiple="true" label="Selection of genome files (fasta)" /> + <conditional name="mode"> + <param name="schema_select" type="select" display="radio" label="Which schema would you like to use as a reference?"> + <option value="system" selected="True">System reference</option> + <option value="user">Own reference</option> + </param> + <when value="system"> + <param name="reference" type="select" label="Choose reference"> + <options from_data_table="chewbbaca_schemas" /> + </param> + </when> + <when value="user"> + <param name="genes" format="txt" type="data" label="File with list of genes (fasta)" /> + </when> + </conditional> + <param name="bsr" type="text" value="0.6" optional="true" label="minimum BSR score" /> + <conditional name="ptfmode"> + <param name="ptf_select" type="select" display="radio" label="Which Prodigal training file would you like to use?"> + <option value="system">System training file</option> + <option value="user">Own training file</option> + <option value="noptf" selected="True">No training file</option> + </param> + <when value="system"> + <param name="ptf_system" type="select" label="Choose Prodigal training file"> + <options from_data_table="chewbbaca_ptfs" /> + </param> + </when> + <when value="user"> + <param name="ptf_user" format="binary" type="data" optional="true" multiple="false" label="Prodigal Training File" /> + </when> + <when value="noptf" /> + </conditional> + <!--<param name="forceContinue" type="boolean" truevalue="true" falsevalue="false" checked="False" label="force continue" />--> + <!--<param name="forceReset" type="boolean" truevalue="true" falsevalue="false" checked="False" label="force reset" />--> + <!--<param name="jsonFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="report in json file" />--> + </when> + <when value="SchemaEvaluator"> + <param name="input1" format="txt" type="data" label="File with list of genes (fasta)" /> + <param name="conserved" type="boolean" truevalue="true" falsevalue="false" checked="False" label="One bad allele still makes gene conserved" /> + <param name="ncbiTA" type="integer" value="11" optional="true" label="ncbi translation table" help="Integer" /> + <param name="threshold" type="float" value="0.05" optional="true" label="Threshold" /> + <param name="title" type="text" value="My Analyzed wg/cg MLST Schema - Rate My Schema" optional="true" label="title on the html plot" /> + <param name="numBoxplots" type="integer" value="500" optional="true" label="number of boxplots per page (more than 500 can make the page very slow)" help="Integer" /> + <param name="light" type="boolean" truevalue="true" falsevalue="false" checked="False" label="skip clustal and mafft run" /> + </when> + <when value="TestGenomeQuality"> + <param name="input1" format="tsv" type="data" label="raw allele call matrix file" /> + <param name="maxNumIterations" type="integer" value="12" label="maximum number of iterations" help="Each iteration removes a set of genomes over the defined threshold (-t) and recalculates all loci presence percentages" /> + <param name="maxThreshold" type="integer" value="200" label="maximum threshold of bad calls above 95 percent" help="This threshold represents the maximum number of missing loci allowed, for each genome independently, before removing it (genome)" /> + <param name="stepThreshold" type="integer" value="5" label="step between each threshold analysis (suggested 5)" help="Integer" /> + </when> + <when value="ExtractCgMLST"> + <param name="input1" format="tsv" type="data" label="input file to clean" /> + <param name="genes" format="txt" type="data" optional="true" label="list of genes to remove, one per line" help="e.g. the list of gene detected by ParalogPrunning.py" /> + <param name="genomes" format="txt" type="data" optional="true" label="list of genomes to remove, one per line" help="e.g. list of genomes to be removed selected based on testGenomeQuality results" /> + <param name="maxPresence" type="float" value="1.0" optional="true" label="maximum presence (e.g 0.95)" > + <validator type="in_range" min="0" max="1" /> + </param> + </when> + <when value="RemoveGenes"> + <param name="input1" format="tsv" type="data" label="main matrix file from which to remove" /> + <param name="genes" format="txt" type="data" label="list of genes to remove" /> + </when> + </conditional> + </inputs> + + <!-- define outputs --> + <outputs> + <data format="txt" name="schema" label="${tool.name}:CreateSchema on ${on_string}" > + <filter>selectFunction['myFunctions'] == "CreateSchema"</filter> + </data> + <data format="tsv" name="statistics" label="${tool.name}:AlleleCall on ${on_string}: Statistics" > + <filter>selectFunction['myFunctions'] == "AlleleCall"</filter> + </data> + <data format="tsv" name="contigsinfo" label="${tool.name}:AlleleCall on ${on_string}: Contigs Info" > + <filter>selectFunction['myFunctions'] == "AlleleCall"</filter> + </data> + <data format="tsv" name="alleles" label="${tool.name}:AlleleCall on ${on_string}: Alleles" > + <filter>selectFunction['myFunctions'] == "AlleleCall"</filter> + </data> + <data format="txt" name="logginginfo" label="${tool.name}:AlleleCall on ${on_string}: Logging info" > + <filter>selectFunction['myFunctions'] == "AlleleCall"</filter> + </data> + <data format="txt" name="repeatedloci" label="${tool.name}:AlleleCall on ${on_string}: Repeated Loci" > + <filter>selectFunction['myFunctions'] == "AlleleCall"</filter> + </data> + <data format="tar" name="schemaplot" label="${tool.name}:SchemaEvaluator on ${on_string}" > + <filter>selectFunction['myFunctions'] == "SchemaEvaluator"</filter> + </data> + <data format="html" name="thresholdplot" from_work_dir="output_dir/GenomeQualityPlot.html" label="${tool.name}:TestGenomeQuality on ${on_string}: Plot" > + <filter>selectFunction['myFunctions'] == "TestGenomeQuality"</filter> + </data> + <data format="tsv" name="removedgenomes" from_work_dir="output_dir/removedGenomes.txt" label="${tool.name}:TestGenomeQuality on ${on_string}: Removed genomes" > + <filter>selectFunction['myFunctions'] == "TestGenomeQuality"</filter> + </data> + <data format="tsv" name="cgmlst" from_work_dir="output_dir/cgMLST.tsv" label="${tool.name}:ExtractCgMLST on ${on_string}: cgMLST" > + <filter>selectFunction['myFunctions'] == "ExtractCgMLST"</filter> + </data> + <data format="txt" name="cgmlstschema" from_work_dir="output_dir/cgMLSTschema.txt" label="${tool.name}:ExtractCgMLST on ${on_string}: cgMLSTschema" > + <filter>selectFunction['myFunctions'] == "ExtractCgMLST"</filter> + </data> + <data format="tsv" name="removedgenes" from_work_dir="output_removegenes.tsv" label="${tool.name}:RemoveGenes on ${on_string}" > + <filter>selectFunction['myFunctions'] == "RemoveGenes"</filter> + </data> + </outputs> + <tests> + <test> + <param name="selectFunction['myFunctions']" value="AlleleCall" /> + <param name="input1" value="a_contigs.fasta" ftype="fasta" /> + <param name="selectFunction.mode['schema_select']" value="system" /> + <param name="selectFunction.mode['reference']" value="schema_pubMLST" /> + <param name="selectFunction.mode['ptf_select']" value="noptf" /> + <output name="statistics" > + <assert_contents> + <has_text text="a_contigs.fasta" /> + </assert_contents> + </output> + </test> + </tests> + <help> +**chewBBACA** stands for "BSR-Based Allele Calling Algorithm". The "chew" part could be thought of as "Comprehensive and Highly Efficient Workflow" +but at this point still it needs a bit of work to make that claim so we just add "chew" to add extra coolness to the software name. +This tool is in beta test. + +The development of the tools have been supported by INNUENDO project (https://www.innuendoweb.org) co-funded by the European Food Safety Authority (EFSA), grant agreement GP/EFSA/AFSCO/2015/01/CT2 +("New approaches in identifying and characterizing microbial and chemical hazards") and by the ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI - “Fundos Europeus Estruturais e de Investimento” +from “Programa Operacional Regional Lisboa 2020” and by national funds from FCT - “Fundação para a Ciência e a Tecnologia” and BacGenTrack (TUBITAK/0004/2014) +[FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBITAK)]. + </help> + <citations> + <citation type="bibtex">@ARTICLE{andrews_s, + author = {Rossi, M and Silva, M and Ribeiro-Gonçalves, B and Silva, DN and Machado, MP and Oleastro, M and Borges, V and Isidro, J and Gomes, JP and Vieira, L and Barker, DOR and Llarena, AK and Halkilahti, + J and Jaakkonen, A and Palma, F and Culebro, A and Kivistö, R and Hänninen, ML and Laukkanen-Ninios, R and Fredriksson-Ahomaa, M and Salmenlinna, S and Hakkinen, M and Garaizer, J and Bikandi, J and Hilbert, + F and Taboada, EN and Carriço, JA}, + keywords = {bioinformatics, ngs, mlst}, + title = {{INNUENDO whole and core genome MLST databases and schemas for foodborne pathogens}}, + url = {https://github.com/TheInnuendoProject/chewBBACA_schemas} + }</citation> + <citation type="doi">10.1099/mgen.0.000166</citation> + <citation type="doi">10.1371/journal.pgen.1007261</citation> + </citations> +</tool>