Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/rarefaction.shared.xml @ 7:7bfe1f843858
Support Mothur v1.20
trim.seqs - added name parameter and optional trim.names output
phylo.diversity - group optional, put group and groups in conditional - breaks
get.lineage remove.lineage - allow multiple taxons
dist.shared - added processors
consensus.seqs - add cutoff parameter
trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs
new tools - chimera.uchime deunique.tree count.seqs
shared/relabund files - Column headings
refactor lib/galaxy/datatypes/metagenomics.py
add filters to label and group selects in tool configs
mothur_wrapper.py updated with new tools params
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 27 Jun 2011 10:12:25 -0500 |
parents | e990ac8a0f58 |
children | d86987601022 |
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<tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.20.0"> <description>Generate inter-sample rarefaction curves for OTUs</description> <command interpreter="python"> mothur_wrapper.py --cmd='rarefaction.shared' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.rarefaction$:'$rarefaction --outputdir='$logfile.extra_files_path' --shared=$otu #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups #end if #if int($iters.__str__) > 0: --iters=$iters #end if $jumble #if $calc.__str__ != "None" and len($calc.__str__) > 0: --calc='$calc' #end if </command> <inputs> <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> <filter type="unique_value" name="unq_lbl" column="0" /> </options> </param> <param name="groups" type="select" label="groups - Groups to analyze" multiple="true"> <help>All groups will be analyzed by default if none are selected</help> <options from_dataset="otu"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> <filter type="unique_value" name="unq_grp" column="1" /> <filter type="add_value" name="all" value="all" /> </options> </param> <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/> <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> <options from_file="mothur_calculators.loc"> <column name="mult2" index="2"/> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="static_value" name="mult2" column="2" value="rare" /> </options> </param> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" /> </outputs> <requirements> <requirement type="binary">mothur</requirement> </requirements> <tests> </tests> <help> **Mothur Overview** Mothur_, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan, provides bioinformatics for the microbial ecology community. .. _Mothur: http://www.mothur.org/wiki/Main_Page **Command Documenation** The rarefaction.shared_ command generates inter-sample rarefaction curves using a re-sampling without replacement approach. The traditional way that ecologists use rarefaction is not to randomize the sampling order within a sample, rather between samples. For instance, if we wanted to know the number of OTUs in the human colon, we might sample from various sites within the colon, and sequence a bunch of 16S rRNA genes. By determining the number of OTUs in each sample and comparing the composition of those samples it is possible to determine how well you have sampled the biodiversity within the individual. For calc parameter choices see: http://www.mothur.org/wiki/Calculators .. _rarefaction.shared: http://www.mothur.org/wiki/Rarefaction.shared </help> </tool>