Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/classify.tree.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
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date | Mon, 10 Nov 2014 15:40:02 -0500 |
parents | 95d75b35e4d2 |
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<tool id="mothur_classify_tree" name="Classify.tree" version="1.25.0"> <description>Get a consensus taxonomy for each node on a tree</description> <command interpreter="python"> mothur_wrapper.py --cmd='classify.tree' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.taxonomy\.tre$:'$out_tree,'^\S+\.taxonomy\.summary$:'$summary --outputdir='$logfile.extra_files_path' --taxonomy=$taxonomy --tree=$tree #if $name.__str__ != "None" and len($name.__str__) > 0: --name='$name' #end if #if $group.__str__ != "None" and len($group.__str__) > 0: --group=$group #end if --name=$names </command> <inputs> <param name="taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> <param name="tree" type="data" format="tre" label="tree - Sequences to filter"/> <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file"/> <param name="group" type="data" format="group" optional="true" label="group - Sequences Group reference"/> <param name="cutoff" type="integer" value="51" optional="true" label="cutoff - consensus confidence threshold" help="The default is 51, meaning 51%. Cutoff cannot be below 51"> <validator type="in_range" message="The percentage cutoff must be between 51 and 100" min="51" max="100"/> </param> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format_source="tree" name="out_tree" label="${tool.name} on ${on_string}: taxonomy.tre" /> <data format_source="tabular" name="summary" label="${tool.name} on ${on_string}: taxonomy.summary" /> </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 classify.tree_ command is used to get a consensus taxonomy for each node on a tree. Input is a taxonomy_ and a tree_ with optional name_ or group_ reference. The output is a tree_ and a summary.. TreeNode NumRep Taxonomy 243 2 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100); 244 3 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100); 245 4 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100); ... .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline .. _tree: http://evolution.genetics.washington.edu/phylip/newicktree.html .. _name: http://www.mothur.org/wiki/Name_file .. _group: http://www.mothur.org/wiki/Group_file .. _classify.tree: http://www.mothur.org/wiki/Classify.tree v.1.25.0: Trivial upgrade to Mothur 1.33 </help> </tool>