Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/phylo.diversity.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 | 4f797d3eee3a |
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<tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.20.0"> <description>Alpha Diversity calculates unique branch length</description> <command interpreter="python"> mothur_wrapper.py --cmd='phylo.diversity' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.phylodiv\.summary$:'$summary_out,'^\S+\.phylodiv$:'$collectors_out,'^\S+\.rarefaction$:'$rarefaction_out --outputdir='$logfile.extra_files_path' --tree=$tree #if $grouping.use: #if $grouping.group.__str__ != "None" and len($grouping.group.__str__) > 0: --group='$grouping.group' #end if #if $grouping.groups.__str__ != "None" and len($grouping.groups.__str__) > 0: --groups='$grouping.groups' #end if #end if #if $name.__str__ != "None" and len($name.__str__) > 0: --name='$name' #end if #if int($iters.__str__) > 0: --iters=$iters #end if #if float($freq.__str__) > 0: --freq=$freq #end if $scale $collect $rarefy #if len($rarefy.__str__) > 0 or len($collect.__str__) > 0: $summary #end if --processors=2 </command> <inputs> <!-- list,group or shared --> <param name="tree" type="data" format="tre" label="tree - Phylogenetic Tree"/> <conditional name="grouping"> <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Analyze by group using a Group file"/> <when value="yes"> <param name="group" type="data" format="groups" label="group - Group file for the tree"/> <param name="groups" type="select" label="groups - Groups to display" multiple="true"> <help>All groups displayed if none are selected.</help> <options from_dataset="group"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="unique_value" name="unq_grp" column="1" /> </options> </param> </when> <when value="no"/> </conditional> <!-- use_groups --> <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file for the tree"/> <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/> <param name="freq" type="float" value="0.0" label="freq - Reporting frequency" help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/> <param name="scale" type="boolean" truevalue="--scale=true" falsevalue="" checked="false" label="scale - Scale output to the number of sequences sampled" /> <param name="rarefy" type="boolean" truevalue="--rarefy=true" falsevalue="" checked="false" label="rarefy - Calculate the rarefaction data" /> <param name="summary" type="boolean" truevalue="" falsevalue="--summary=false" checked="true" label="summary - Generate a summary file" /> <param name="collect" type="boolean" truevalue="--collect=true" falsevalue="" checked="false" label="collect - Create a collectors curve" /> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="summary_out" label="${tool.name} on ${on_string}: summary"> <filter>summary == True</filter> </data> <data format="tabular" name="rarefaction_out" label="${tool.name} on ${on_string}: rarefaction"> <filter>rarefy == True</filter> </data> <data format="tabular" name="collectors_out" label="${tool.name} on ${on_string}: collectors"> <filter>collect == True</filter> </data> <!-- random uses input prompts, not sure how to model that <data format="tabular" name="random" label="${tool.name} on ${on_string}: random"> </data> --> </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 phylo.diversity_ command calculates alpha diversity as the total of the unique branch length. .. _phylo.diversity: http://www.mothur.org/wiki/Phylo.diversity </help> </tool>