Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/merge.groups.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
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<tool id="mothur_merge_groups" name="Merge.groups" version="1.24.0" > <description>Merge groups in a shared file</description> <command interpreter="python"> mothur_wrapper.py --cmd='merge.groups' ## 98_sq_phylip_amazon.fn.merge.shared #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] --outputdir='$logfile.extra_files_path' #if $otu.__str__ != "None" and len($otu.__str__) > 0: --shared=$otu #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.merge.\2',$os.path.basename($otu.__str__)) + ":'" + $merge_shared.__str__] #end if #if $group.__str__ != "None" and len($group.__str__) > 0: --group=$group #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.merge.\2',$os.path.basename($group.__str__)) + ":'" + $merge_group.__str__] #end if #if $design.source == 'hist': --design=$design_dataset #else: --design=$generated_design #end if #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups #end if #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if --result=#echo ','.join($results) </command> <inputs> <param name="otu" type="data" format="shared" optional="true" label="shared - OTU Shared Dataset"/> <param name="group" type="data" format="groups" optional="true" label="group - Group Dataset"/> <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> <options> <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" multiple="true"> <options> <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <conditional name="design"> <param name="source" type="select" label="Grouping Design from" help=""> <option value="hist">Your History</option> <option value="build">Build a grouping design</option> </param> <when value="hist"> <param name="design_dataset" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/> </when> <when value="build"> <repeat name="groupings" title="Grouping"> <param name="name" type="text" label="Name for a new combined grouping"/> <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping"> <options> <filter type="data_meta" ref="otu" key="groups" /> </options> </param> </repeat> </when> </conditional> <!-- design --> </inputs> <configfiles> <configfile name="generated_design"> #if $design.source == 'build': #for $grouping in $design.groupings: #set grp_str = $grouping.groups.__str__ #if grp_str != None and len(grp_str) > 0: #for $grp in grp_str.split(','): $grp $grouping.name #end for #end if #end for #end if </configfile> </configfiles> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="shared" name="merged_shared" label="${tool.name} on ${on_string}: merge.shared" > <filter>otu != None</filter> </data> <data format="groups" name="merged_group" label="${tool.name} on ${on_string}: merge.groups" > <filter>groups != None</filter> </data> </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 merge.groups_ command reads a shared_ file and a design file and merges the groups in the shared file that are in the same grouping in the design file. A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. : ======= ======= duck bird cow mammal pig mammal goose bird cobra reptile ======= ======= The Make_Design tool can construct a design file from a Mothur dataset that contains group names. .. _shared: http://www.mothur.org/wiki/Shared_file .. _merge.groups: http://www.mothur.org/wiki/Merge.groups </help> </tool>