Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/get.oturep.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_get_oturep" name="Get.oturep" version="1.23.0" force_history_refresh="true"> <description>Generate a fasta with a representative sequence for each OTU</description> <command interpreter="python"> mothur_wrapper.py --cmd='get.oturep' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' #if $as_datasets.__str__ == "yes": --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:${fasta.ext}','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names' #end if #if $fasta.__str__ != "None" and len($fasta.__str__) > 0: --fasta=$fasta #end if --list=$otu_list #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 #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if #if $pick.type == 'yes': #if $pick.group.__str__ != "None" and len($pick.group.__str__) > 0: --group=$pick.group #end if #if $pick.groups.__str__ != "None" and len($pick.groups.__str__) > 0: --groups=$pick.groups #end if #end if #if $sorted.__str__ != "None" and len($sorted.__str__) > 0: --sorted=$sorted #end if #if $method.__str__ != "None" and len($method.__str__) > 0: --method=$method #end if $large #if $count.__str__ != "None" and len($count.__str__) > 0: --count=$count #end if </command> <inputs> <!-- get.relabund relabund type should also work --> <param name="otu_list" type="data" format="list" label="list - OTU List"/> <conditional name="input"> <param name="source" type="select" label="Distance Matrix Format"> <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> </conditional> <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Fasta"/> <conditional name="pick"> <param name="type" type="select" label="Parse a group file into abundant and rare groups?" help=""> <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param name="group" type="data" format="groups" label="group - Group file for the OTU List"/> <param name="groups" type="select" label="groups - Group Selection (all used if none are selected)" multiple="true"> <options> <filter type="data_meta" ref="group" key="groups" /> </options> </param> </when> </conditional> <!-- pick --> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options> <filter type="data_meta" ref="otu_list" key="labels" /> </options> </param> <param name="sorted" type="select" label="sorted - Sort Sequences by"> <option value="">Don't sort</option> <option value="name">Sequence Name</option> <option value="number">Bin Number</option> <option value="size">Bin Size</option> <option value="group">Group</option> </param> <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Distance Matrix is very Large"/> <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label"/> <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> <param name ="method" type="select" label="method - select the method of selecting the representative sequence" help="the distance method finds the sequence with the smallest maximum distance to other sequences. The abundance method chooses the abundant sequence in the OTU as the representative" optional = "true"> <option value="distance">distance</option> <option value="abundance">abundance</option> </param> </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 get.oturep_ command generates a fasta-formatted sequence file containing only a representative sequence for each OTU. The opposite of the bin.seqs command. .. _get.oturep: http://www.mothur.org/wiki/Get.oturep v1.23.0: Updated to Mothur 1.33, added count and method parameter </help> </tool>