Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/phylo.diversity.xml @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author | certain cat |
---|---|
date | Fri, 31 Oct 2014 15:09:32 -0400 |
parents | 49058b1f8d3f |
children |
line wrap: on
line source
<tool id="mothur_phylo_diversity" name="Phylo.diversity" version="1.21.0"> <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=8 #if $count.__str__ != "None" and len($count.__str__) > 0: --count=$count #end if </command> <inputs> <!-- list,group or shared --> <param name="tree" type="data" format="tre" label="tree - Phylogenetic Tree"/> <conditional name="grouping"> <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Analyze by group using a Group file"/> <when value="yes"> <param name="group" type="data" format="groups" label="group - Group file for the tree"/> <param name="groups" type="select" label="groups - Groups to display" multiple="true"> <help>All groups displayed if none are selected.</help> <options> <filter type="data_meta" ref="group" key="groups" /> </options> </param> </when> <when value="no"/> </conditional> <!-- use_groups --> <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file for the tree"/> <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/> <param name="freq" type="float" value="0.0" label="freq - Reporting frequency" help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/> <param name="scale" type="boolean" truevalue="--scale=true" falsevalue="" checked="false" label="scale - Scale output to the number of sequences sampled" /> <param name="rarefy" type="boolean" truevalue="--rarefy=true" falsevalue="" checked="false" label="rarefy - Calculate the rarefaction data" /> <param name="summary" type="boolean" truevalue="" falsevalue="--summary=false" checked="true" label="summary - Generate a summary file" /> <param name="collect" type="boolean" truevalue="--collect=true" falsevalue="" checked="false" label="collect - Create a collectors curve" /> <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${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 = "package" version ="1.33">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 v.1.21.0: Updated to Mothur 1.33, added count parameter </help> </tool>