Mercurial > repos > iuc > mothur_chimera_uchime
diff chimera.uchime.xml @ 2:d1e70be881e5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 22:21:36 -0400 |
parents | 6dc4f9beec9f |
children | 4e3780d096af |
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--- a/chimera.uchime.xml Tue Sep 05 17:00:36 2017 -0400 +++ b/chimera.uchime.xml Tue Mar 20 22:21:36 2018 -0400 @@ -7,129 +7,151 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@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 "$template.reference" template.reference.dat && - #end if +## create symlinks to input datasets +ln -s '$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 +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 name="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Aligned Sequences"/> + <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" help=""> + <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 name="reference" type="select" label="reference - Select an alignment database " help=""> - <options from_data_table="mothur_aligndb"> - </options> + <param argument="reference" type="select" label="reference - Select an alignment database"> + <options from_data_table="mothur_aligndb"/> </param> </when> <when value="hist"> - <param name="reference" type="data" format="fasta" label="reference - Reference to align with" help=""/> + <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/> </when> <when value="self"> - <param name="abskew" type="float" value="1.9" label="abskew - Abundance skew (default 1.9)" help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query)"/> - <param name="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 name="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 *.pick.count_table file containing seqeunces after chimeras are removed."/> + <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 name="name" type="data" format="mothur.names" label="name - Sequence names"/> + <param argument="name" type="data" format="mothur.names" label="name - Sequence names"/> </when> </conditional> - <param name="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups, default=f" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/> - <param name="skipgaps" type="boolean" falsevalue="false" truevalue="true" checked="true" label="skipgaps - columns containing gaps do not count as diffs. Default=T" help="controls how gapped columns affect counting of diffs"/> - <param name="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. Default=T" help="controls how gapped columns affect counting of diffs"/> - <param name="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 name="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 name="mindiv" type="float" value="0.5" min="0" label="mindiv - minimum divergence ratio, default 0.5" help="to ignore very close chimeras, increase mindiv to 1.0 or 2.0, to increase sensitivity decrease minh to 0.1"/> - <param name="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 name="dn" type="float" value="1.4" min="0" label="dn - pseudo-count prior on number of no votes. Default 1.4" help="Reasonable values are probably in the range from 0.2 to 2.0"/> - <param name="xa" type="float" value="1.0" min="0" label="xa - eight of an abstain vote. Default 1.0" help="Reasonable values might range from 0.1 to 2.0"/> - <param name="chunks" type="integer" value="4" min="0" label="chunks - number of chunks. Default 4." help="number of chunks to extract from the query sequence when searching for parents."/> - <param name="minchunk" type="integer" value="64" min="0" label="minchunk - minimum length of a chunk. Default 64." help=""/> - <param name="maxp" type="integer" value="2" min="0" label="maxp - maximum number of candidate parents to consider. Default 2" help="increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit"/> - <param name="minlen" type="integer" value="10" min="0" label="minlen - minimum unaligned sequence length. Default 10" help="Applies to both query and reference sequences."/> - <param name="maxlen" type="integer" value="10000" min="0" label="maxlen - maximum unaligned sequence length. Defaults 10000" help="Applies to both query and reference sequences."/> - <param name="idsmoothwindow" type="integer" value="32" min="0" optional="True" label="idsmoothwindow - the length of id smoothing window. Default 32" help=""/> + <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 name="ucl" type="select" label="ucl - Use local-X alignments" help="global-X is the default"> + <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 name="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. Default 0.5." help=""/> + <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="out_file" format="txt" from_work_dir="fasta.*uchime.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/> + <data name="uchime.chimeras" format="txt" from_work_dir="fasta.*uchime.chimeras" label="${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['count']</filter> + <filter>template['source'] == 'self' and template['count']</filter> </data> </outputs> <tests> @@ -137,15 +159,17 @@ <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="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras" ftype="txt"/> + <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="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras" ftype="txt"/> + <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 --> @@ -153,14 +177,14 @@ <param name="source" value="hist"/> <param name="reference" value="HMP_MOCK.v35.align"/> <param name="chimealns" value="true"/> - <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras" ftype="txt"/> + <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[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -171,7 +195,7 @@ .. _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> + + ]]></help> <expand macro="citations"/> </tool>