Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/dist.shared.xml @ 32:ec8df51e841a
Fixes courtesy of Peter Briggs:
metagenomics.py:
- Groups class: Fix for when second column not present
- Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular
data uploads being sniffed as this type
mothur_wrapper.py:
- update cmd_dict['chimera.perseus'], to use correct inputs
- add --beta option (needed for chimera.perseus tool)
- add function for converting input floats from scientific notation (e.g. 1e-6,
which mothur can't handle) to decimal format (e.g. 0.00001, which it can)
chimera.perseus.xml:
- add output data item for the "accnos" file (not previous captured in the
history)
trim.flows.xml:
- cosmetic change: base name for additional output data items is now "trim.flows",
rather than "logfile" (clarifies history items)
shhh.flows.xml:
- cosmetic change: update default value specified in help for mindiff to be
consistent with that given in the mothur documentation
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Wed, 04 Sep 2013 10:51:34 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
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<tool id="mothur_dist_shared" name="Dist.shared" version="1.25.0" force_history_refresh="True"> <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description> <command interpreter="python"> mothur_wrapper.py --cmd='dist.shared' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' #if $as_datasets.__str__ == "yes": --datasetid='$logfile.id' --new_file_path='$__new_file_path__' #if len($output.__str__) > 0: #if $output.__str__ == 'square': --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt)(\.(ave|std))?)\.dist$:square.dist' #elif $output.__str__ == 'lt': --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt)(\.(ave|std))?)\.dist$:lower.dist' #end if #else: --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt)(\.(ave|std))?)\.dist$:lower.dist' #end if #end if --shared=$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 $calc.__str__ != "None" and len($calc.__str__) > 0: --calc=$calc #end if #if $subsampling.use: #if len($subsampling.subsample.__str__) > 0 and int($subsampling.subsample.__str__) > 0: --subsample=$subsampling.subsample #else --subsample=T #end if #if len($subsampling.iters.__str__) > 0 and int($subsampling.iters.__str__) > 0: --iters=$subsampling.iters #end if #end if #if $output.__str__ != "None" and len($output.__str__) > 0: --output=$output #end if --processors=8 </command> <inputs> <!-- list,group or shared --> <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true"> <options> <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to analyze" multiple="true"> <options> <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> <option value="sharedace">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">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">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> <option value="sorest">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">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">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> <option value="thetan">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> <conditional name="subsampling"> <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="subsample"/> <when value="yes"> <param name="subsample" type="integer" value="" optional="true" label="subsample (defaults to the size of the smallest group)" help="Should not exceed the number of sequences in any group"/> <param name="iters" type="integer" value="" optional="true" label="iters - Number of iterations to try (default 1000)"> <validator type="in_range" message="Number of iterations must be positive" min="1"/> </param> </when> <when value="no"/> </conditional> <!-- subsampling --> <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair"> <option value="lt">Phylip formatted Lower Triangle Matrix</option> <option value="square">Phylip formatted Square Matrix</option> </param> <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each distance matrix"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> <requirement type="package" version="1.27">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 dist.shared_ command will generate a phylip-formatted_distance_matrix_ that describes the dissimilarity (1-similarity) among multiple groups from a shared_ file. For calc parameter choices see: http://www.mothur.org/wiki/Calculators .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _shared: http://www.mothur.org/wiki/Shared_file .. _dist.shared: http://www.mothur.org/wiki/Dist.shared </help> </tool>