Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/parse.list.xml @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author | certain cat |
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date | Fri, 31 Oct 2014 15:09:32 -0400 |
parents | 49058b1f8d3f |
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<tool id="mothur_parse_list" name="Parse.list" version="1.19.0" force_history_refresh="True"> <description>Generate a List file for each group</description> <command interpreter="python"> mothur_wrapper.py --cmd='parse.list' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.(\S+\.list)$:list' --list=$otu --group=$group #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if #if $count.__str__ != "None" and len($count.__str__) > 0: --count=$count #end if </command> <inputs> <param name="otu" type="data" format="list" label="list - OTU List"/> <param name="group" type="data" format="groups" label="group - Sequences Name reference"/> <param name="label" type="select" optional="true" label="label - To filter: Select OTU Labels to include" multiple="true"> <help>All labels are included if none are selected</help> <options> <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </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 parse.list_ command reads a list_ file and group_ file and generates a list_ file for each group_ in the groupfile. .. _list: http://www.mothur.org/wiki/List_file .. _group: http://www.mothur.org/wiki/Group_file .. _parse.list: http://www.mothur.org/wiki/Parse.list v.1.19.0: Updated to mothur 1.33, added count parameter </help> </tool>