Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/collect.shared.xml @ 19:d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Tue, 17 Jan 2012 14:16:44 -0600 |
parents | 7bfe1f843858 |
children | ed906f8149bb |
line wrap: on
line source
<tool id="mothur_collect_shared" name="Collect.shared" version="1.20.0" force_history_refresh="True"> <description>Generate collector's curves for calculators on OTUs</description> <command interpreter="python"> mothur_wrapper.py --cmd='collect.shared' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.(anderberg|braycurtis|jabund|jclass|jest|kstest|kulczynski|kulczynskicody|lennon|morisitahorn|ochiai|shared\.ace|shared\.chao|shared\.nseqs|shared\.sobs|sorabund|sorclass|sorest|thetan|thetayc|whittaker)$:tabular' --shared=$otu #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if #if $calc.__str__ != "None" and len($calc.__str__) > 0: --calc='$calc' #end if $all #if float($freq.__str__) > 0: --freq=$freq #end if #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups #end if </command> <inputs> <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> <param name="label" type="select" label="label - OTU Label filter" multiple="true"> <help>To filter: select labels to include</help> <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 filter (uses all groups if none are selected)" multiple="true"> <help>To filter: select select at least 2 groups</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" /> </options> </param> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none are selected)" multiple="true"> <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option> <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option> <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option> <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option> <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option> <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option> <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option> <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> <option value="hamming">hamming - Community Membership Similarity -</option> <option value="memchi2">memchi2 - Community Membership Similarity -</option> <option value="memchord">memchord - Community Membership Similarity -</option> <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option> <option value="mempearson">mempearson - Community Membership Similarity -</option> <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option> <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option> <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> <option value="canberra">canberra - Community Structure Similarity -</option> <option value="gower">gower - Community Structure Similarity -</option> <option value="hellinger">hellinger - Community Structure Similarity -</option> <option value="manhattan">manhattan - Community Structure Similarity -</option> <option value="odum">odum - Community Structure Similarity -</option> <option value="soergel">soergel - Community Structure Similarity -</option> <option value="spearman">spearman - Community Structure Similarity -</option> <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option> <option value="structchi2">structchi2 - Community Structure Similarity -</option> <option value="structchord">structchord - Community Structure Similarity -</option> <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option> <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option> <option value="structpearson">structpearson - Community Structure Similarity -</option> <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option> <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option> </param> <param name="freq" type="float" value="0.0" label="freq - "/> <param name="all" type="boolean" truevalue="--all=true" falsevalue="" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </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 collect.shared_ command generates collector's curves for calculators_, which describe the similarity between communities or their shared richness. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. For calc parameter choices see: http://www.mothur.org/wiki/Calculators .. _calculators: http://www.mothur.org/wiki/Calculators .. _collect.shared: http://www.mothur.org/wiki/Collect.shared </help> </tool>