Mercurial > repos > iuc > mothur_chimera_slayer
diff chimera.slayer.xml @ 2:6f7f890e6a54 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 21:55:10 -0400 |
| parents | 72b33fe8c05a |
| children | a899cc1416bc |
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--- a/chimera.slayer.xml Tue Sep 05 17:07:29 2017 -0400 +++ b/chimera.slayer.xml Tue Mar 20 21:55:10 2018 -0400 @@ -7,124 +7,129 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## enable mothur to find blast - loc=`which mothur` && ln -s "\${loc%/mothur}"/* . && +## enable mothur to find blast +ln -s ln -s `dirname \$(which mothur)`/* . && - ## create symlinks to input datasets - ln -s "$fasta" fasta.dat && - #if $alignment.source == "self": - ln -s "$alignment.name" alignment.name.dat && - ln -s "$alignment.group" alignment.group.dat && - ln -s "$alignment.count" alignment.count.dat && - #else: - ln -s "$alignment.template" alignment.template.dat && - #end if +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && +#if $alignment.source == "self": + ln -s '$alignment.name' alignment.name.dat && + ln -s '$alignment.group' alignment.group.dat && + ln -s '$alignment.count' alignment.count.dat && +#else: + ln -s '$alignment.reference' alignment.reference.dat && +#end if - echo 'chimera.slayer( - fasta=fasta.dat, - #if $alignment.source == "self": - reference=self, - #if $alignment.name: - name=$alignment.name, - #end if - #if $alignment.group: - group=$alignment.group, - #end if - #if $alignment.count: - count=$alignment.count, - #end if - #else: - reference=$alignment.template, - #end if - #if $options.setby == "user": - search=$options.search, - window=$options.window, - increment=$options.increment, - match=$options.match, - mismatch=$options.mismatch, - numwanted=$options.numwanted, - parents=$options.parents, - minsim=$options.minsim, - mincov=$options.mincov, - iters=$options.iters, - minbs=$options.minbs, - minsnp=$options.minsnp, - divergence=$options.divergence, - trim=$options.trim, - split=$options.split, - #end if - dereplicate=$dereplicate, - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | ./mothur - | tee mothur.out.log +echo 'chimera.slayer( + fasta=fasta.dat, + #if $alignment.source == "self": + reference=self, + #if $alignment.name: + name=$alignment.name, + #end if + #if $alignment.group: + group=$alignment.group, + #end if + #if $alignment.count: + count=$alignment.count, + #end if + #else: + reference=$alignment.reference, + #end if + #if $options.setby == "user": + search=$options.search, + window=$options.window, + increment=$options.increment, + match=$options.match, + mismatch=$options.mismatch, + numwanted=$options.numwanted, + parents=$options.parents, + minsim=$options.minsim, + mincov=$options.mincov, + iters=$options.iters, + minbs=$options.minbs, + minsnp=$options.minsnp, + divergence=$options.divergence, + trim=$options.trim, + split=$options.split, + #end if + dereplicate=$dereplicate, + processors='\${GALAXY_SLOTS:-8}' +)' +| sed 's/ //g' ## mothur trips over whitespace +| ./mothur +| tee mothur.out.log ]]></command> <inputs> - <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> + <param argument="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> <conditional name="alignment"> - <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 - Use abundant sequences from the input Candiate Sequences fasta </option> </param> <when value="ref"> - <param name="template" type="select" label="reference - Select an alignment database " help=""> + <param argument="reference" type="select" label="reference - Select an alignment database"> <options from_data_table="mothur_aligndb"> </options> </param> </when> <when value="hist"> - <param name="template" 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="count" type="data" format="mothur.count_table" optional="true" label="count - Count file"/> - <param name="name" type="data" format="mothur.names" optional="true" label="names - Sequences Names"/> - <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 argument="count" type="data" format="mothur.count_table" optional="true" label="count - Count file"/> + <param argument="name" type="data" format="mothur.names" optional="true" label="names - Sequences Names"/> + <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"/> </when> </conditional> <conditional name="options"> - <param name="setby" type="select" label="Slayer Options" help=""> + <param name="setby" type="select" label="Slayer Options"> <option value="default">Use default settings</option> <option value="user">Manually set options</option> </param> <when value="default"/> <when value="user"> - <param name="search" type="select" label="search - Search method for finding the closest parent" help=""> + <param argument="search" type="select" label="search - Search method for finding the closest parent"> <option value="blast" selected="true">blast</option> <option value="kmer">kmer</option> </param> - <param name="window" type="integer" value="50" label="window - Window size for searching for chimeras (default 50)"/> - <param name="increment" type="integer" value="5" label="increment - Increment for window slide on each iteration (default 5)"/> - <param name="match" type="integer" value="5" label="match - Reward matched bases (default 5)"/> - <param name="mismatch" type="integer" value="-4" label="mismatch - Penalty for mismatched bases (default -4)"/> - <param name="numwanted" type="integer" value="15" label="numwanted - Number of potential parents to to compare with query sequence (default 15)"/> - <param name="parents" type="integer" value="3" label="parents - Number of potential parents to investigate from the numwanted best matches"/> - <param name="minsim" type="integer" value="90" label="minsim - Minimum similarity % between the query and parent (default 90)"/> - <param name="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in reference and the query (default 70)"/> - <param name="iters" type="integer" value="1000" label="iters - Number of bootstrap iterations to try (default 100)"/> - <param name="minbs" type="integer" value="90" label="minbs - Minimum bootstrap support % for calling a sequence chimeric (default 90)"/> - <param name="minsnp" type="integer" value="10" label="minsnp - Percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default 100)"/> - <param name="divergence" type="float" value="1.007" label="divergence - Divergence cutoff for chimera determination (default 1.007)"/> - <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="false" label="trim - include chimeric sequences trimmed to their longest peice"/> - <param name="split" type="boolean" truevalue="true" falsevalue="false" checked="false" label="split - detect tri- and quadmeras" help="if a sequence comes back as non-chimeric, mothur will test the two sides to see if they are chimeric."/> + <param argument="window" type="integer" value="50" label="window - Window size for searching for chimeras (default 50)"/> + <param argument="increment" type="integer" value="5" label="increment - Increment for window slide on each iteration (default 5)"/> + <param argument="match" type="integer" value="5" label="match - Reward matched bases (default 5)"/> + <param argument="mismatch" type="integer" value="-4" label="mismatch - Penalty for mismatched bases (default -4)"/> + <param argument="numwanted" type="integer" value="15" label="numwanted - Number of potential parents to to compare with query sequence (default 15)"/> + <param argument="parents" type="integer" value="3" label="parents - Number of potential parents to investigate from the numwanted best matches"/> + <param argument="minsim" type="integer" value="90" label="minsim - Minimum similarity % between the query and parent (default 90)"/> + <param argument="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in reference and the query (default 70)"/> + <param argument="iters" type="integer" value="1000" label="iters - Number of bootstrap iterations to try (default 1000)"/> + <param argument="minbs" type="integer" value="90" label="minbs - Minimum bootstrap support % for calling a sequence chimeric (default 90)"/> + <param argument="minsnp" type="integer" value="10" label="minsnp - Percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default 10)"/> + <param argument="divergence" type="float" value="1.007" label="divergence - Divergence cutoff for chimera determination (default 1.007)"/> + <param argument="trim" type="boolean" truevalue="true" falsevalue="false" checked="false" label="trim - include chimeric sequences trimmed to their longest piece"/> + <param argument="split" type="boolean" truevalue="true" falsevalue="false" checked="false" label="split - detect tri- and quadmeras" + help="if a sequence comes back as non-chimeric, mothur will test the two sides to see if they are chimeric."/> </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="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"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> - <data name="out_file" from_work_dir="fasta.slayer.chimeras" format="txt" label="${tool.name} on ${on_string}: slayer.chimeras"/> + <data name="slayer.chimeras" from_work_dir="fasta.slayer.chimeras" format="txt" label="${tool.name} on ${on_string}: slayer.chimeras"/> <data name="out_accnos" from_work_dir="fasta.slayer.accnos" format="mothur.accnos" label="${tool.name} on ${on_string}: slayer.accnos"/> </outputs> <tests> <test><!-- test with external reference --> <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> <param name="source" value="hist"/> - <param name="template" value="HMP_MOCK.v35.align"/> - <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.slayer.chimeras" ftype="txt"/> + <param name="reference" value="HMP_MOCK.v35.align"/> + <output name="slayer.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.slayer.chimeras" ftype="txt"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with self as reference --> @@ -133,13 +138,12 @@ <param name="setby" value="user"/> <param name="search" value="kmer"/> <param name="name" value="HMP_MOCK.v35.align.names"/> - <output name="out_file" file="HMP_MOCK.v35.slayer.chimeras" ftype="txt"/> + <output name="slayer.chimeras" file="HMP_MOCK.v35.slayer.chimeras" ftype="txt"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -163,7 +167,6 @@ .. _ChimeraSlayer: http://microbiomeutil.sourceforge.net/ .. _chimera.slayer: https://www.mothur.org/wiki/Chimera.slayer -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>