Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/tree.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_tree_shared" name="Tree.shared" version="1.20.0" force_history_refresh="True"> <description>Generate a newick tree for dissimilarity among groups</description> <command interpreter="python"> mothur_wrapper.py --cmd='tree.shared' #if $input.source == 'shared': --result='^mothur.\S+\.logfile$:'$logfile #if $input.as_datasets.__str__ == "yes": --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?([a-z]+\.(unique|[0-9.]*)\.tre)$:tre' #end if --shared=$input.dist #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: --groups=$input.groups #end if #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: --label='$input.label' #end if #else: --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tre --outputdir='$logfile.extra_files_path' #if $input.source == 'column': --column=$input.dist --name=$input.name #elif $input.source == 'phylip': --phylip=$input.dist #if $input.name.__str__ != "None" and len($input.name.__str__) > 0: --name=$input.name #end if #end if #end if #if $calc.__str__ != "None" and len($calc.__str__) > 0: --calc=$calc #end if </command> <inputs> <!-- column,name phylip or shared --> <conditional name="input"> <param name="source" type="select" label="Select input format"> <option value="shared">OTU Shared</option> <option value="column">Pairwise Column Distance Matrix</option> <option value="phylip">Phylip Distance Matrix</option> </param> <when value="column"> <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> <param name="name" type="data" format="names" label="name - Sequences Name reference"/> </when> <when value="phylip"> <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> <param name="name" type="data" format="names" optional="true" label="name - Names"/> </when> <when value="shared"> <param name="dist" type="data" format="shared" label="shared - OTU Shared"/> <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label and calculator"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="dist"> <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 consider" multiple="true"> <options from_dataset="dist"> <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> </when> </conditional> <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="shar" /> </options> </param> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tre" name="tre" label="${tool.name} on ${on_string}: tre"> <filter>input['source'] != 'shared'</filter> </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 tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. For calc parameter choices see: http://www.mothur.org/wiki/Calculators .. _tree.shared: http://www.mothur.org/wiki/Tree.shared </help> </tool>