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author | iuc |
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date | Mon, 17 Jun 2024 12:33:33 +0000 |
parents | 4e3780d096af |
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<tool profile="16.07" id="mothur_chimera_uchime" name="Chimera.uchime" version="@WRAPPER_VERSION@.0"> <description>Find putative chimeras using uchime</description> <macros> <import>macros.xml</import> </macros> <expand macro="biotools"/> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @SHELL_OPTIONS@ ## create symlinks to input datasets ln -s '$fasta' fasta.dat && #if $template.source == "self": ln -s '$template.count' template.count.dat && ln -s '$template.group' template.group.dat && #elif $template.source == "names": ln -s '$template.name' template.name.dat && #else: ln -s '$template.reference' template.reference.dat && #end if echo 'chimera.uchime( fasta=fasta.dat, #if $template.source == "self": reference=self, #if float($template.abskew) > 0: abskew=$template.abskew, #end if #if $template.group: group=template.group.dat, #end if #if $template.count: count=template.count.dat, #end if #elif $template.source == "names": name=template.name.dat, #else: reference=template.reference.dat, #end if minh=$minh, mindiv=$mindiv, xn=$xn, dn=$dn, xa=$xa, chunks=$chunks, minchunk=$minchunk, #if $idsmoothwindow: idsmoothwindow=$idsmoothwindow, #end if maxp=$maxp, minlen=$minlen, maxlen=$maxlen, skipgaps=$skipgaps, skipgaps2=$skipgaps2, #if $alignment.ucl == "local": ucl=true, #if $alignment.queryfract: queryfract=$alignment.queryfract, #end if #end if dereplicate=$dereplicate, chimealns=$chimealns, processors='\${GALAXY_SLOTS:-8}' )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log 2>&1 ## uchime component writes output to stderr ]]></command> <inputs> <param argument="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Aligned Sequences"/> <conditional name="template"> <param name="source" type="select" label="Select Reference Template from"> <option value="hist">History</option> <option value="ref">Cached Reference</option> <option value="self">Self</option> <option value="names">Use a names file</option> </param> <when value="ref"> <param argument="reference" type="select" label="reference - Select an alignment database"> <options from_data_table="mothur_aligndb"/> </param> </when> <when value="hist"> <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/> </when> <when value="self"> <param argument="abskew" type="float" value="1.9" label="abskew - Abundance skew" help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query). Default 1.9"/> <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference" help="use the more abundant sequences from the same sample to check the query sequence"/> <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="Generated by count.seqs. When you use a count file with group info and dereplicate=T, mothur will create a count table containing seqeunces after chimeras are removed."/> </when> <when value="names"> <param argument="name" type="data" format="mothur.names" label="name - Sequence names"/> </when> </conditional> <param argument="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups?" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/> <param argument="skipgaps" type="boolean" falsevalue="false" truevalue="true" checked="true" label="skipgaps - columns containing gaps do not count as diffs" help="controls how gapped columns affect counting of diffs"/> <param argument="skipgaps2" type="boolean" falsevalue="false" truevalue="true" checked="true" label="skipgaps2 - column is immediately adjacent to a column containing a gap, it is not counted as a diff" help="controls how gapped columns affect counting of diffs"/> <param argument="chimealns" type="boolean" falsevalue="false" truevalue="true" checked="false" label="chimealns - Produce a file containing multiple alignments of query sequences to parents in human readable format" help="Alignments show columns with differences that support or contradict a chimeric model."/> <param argument="minh" type="float" value="0.3" min="0" label="minh - mininum score to report chimera. Default 0.3" help="Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives."/> <param argument="mindiv" type="float" value="0.5" min="0" label="mindiv - minimum divergence ratio" help="to ignore very close chimeras, increase mindiv to 1.0 or 2.0, to increase sensitivity decrease minh to 0.1. Default 0.5"/> <param argument="xn" type="float" value="8.0" min="0" label="xn - weight of a no vote. Default 8.0" help="Decreasing this weight to around 3 or 4 may give better performance on denoised data"/> <param argument="dn" type="float" value="1.4" min="0" label="dn - pseudo-count prior on number of no votes" help="Reasonable values are probably in the range from 0.2 to 2.0. Default 1.4"/> <param argument="xa" type="float" value="1.0" min="0" label="xa - eight of an abstain vote" help="Reasonable values might range from 0.1 to 2.0. Default 1.0"/> <param argument="chunks" type="integer" value="4" min="0" label="chunks - number of chunks" help="number of chunks to extract from the query sequence when searching for parents. Default 4."/> <param argument="minchunk" type="integer" value="64" min="0" label="minchunk - minimum length of a chunk" help="Default 64"/> <param argument="maxp" type="integer" value="2" min="0" label="maxp - maximum number of candidate parents to consider" help="increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit. Default 2"/> <param argument="minlen" type="integer" value="10" min="0" label="minlen - minimum unaligned sequence length" help="Applies to both query and reference sequences. Default 10"/> <param argument="maxlen" type="integer" value="10000" min="0" label="maxlen - maximum unaligned sequence length" help="Applies to both query and reference sequences. Default 10000"/> <param argument="idsmoothwindow" type="integer" value="32" min="0" optional="True" label="idsmoothwindow - the length of id smoothing window" help="Default 32"/> <conditional name="alignment"> <param argument="ucl" type="select" label="ucl - Use local-X alignments" help="global-X is the default"> <option value="global" selected="true">global</option> <option value="local">local</option> </param> <when value="global"/> <when value="local"> <param argument="queryfract" type="float" value="0.5" min="0" max="1" label="queryfract - minimum fraction of the query sequence that must be covered by a local-X alignment" help="Default 0.5"/> </when> </conditional> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="uchime.chimeras" format="txt" from_work_dir="fasta.*uchime.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/> <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*uchime.accnos" label="${tool.name} on ${on_string}: uchime.accnos"/> <data name="out_alns" format="txt" from_work_dir="fasta.*uchime.alns" label="${tool.name} on ${on_string}: uchime.alns"> <filter>chimealns</filter> </data> <data name="out_count" format="mothur.count_table" from_work_dir="template.*uchime.pick.count_table" label="${tool.name} on ${on_string}: uchime.count_table"> <filter>template['source'] == 'self' and template['count']</filter> </data> </outputs> <tests> <test><!-- default params test --> <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera"/> <param name="source" value="hist"/> <param name="reference" value="HMP_MOCK.v35.align"/> <output name="uchime.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras" ftype="txt"/> <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos" ftype="mothur.accnos"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- de novo test --> <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> <param name="source" value="self"/> <output name="uchime.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras" ftype="txt"/> <output name="out_accnos" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.accnos"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- with chimealns output --> <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera"/> <param name="source" value="hist"/> <param name="reference" value="HMP_MOCK.v35.align"/> <param name="chimealns" value="true"/> <output name="uchime.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras" ftype="txt"/> <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos" ftype="mothur.accnos"/> <output name="out_alns" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.alns" ftype="txt"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The chimera.uchime_ command reads a fasta file and reference file and outputs potentially chimeric sequences. The original uchime program was written by Robert C. Edgar and donated to the public domain, http://drive5.com/uchime .. _chimera.uchime: https://www.mothur.org/wiki/Chimera.uchime Version 1.23.0: Upgrades tool dependency to mothur 1.33 and adds support for count (mothur 1.28) and dereplicate (mothur 1.29) options. ]]></help> <expand macro="citations"> <citation type="doi">10.1093/bioinformatics/btr381</citation> </expand> </tool>