Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/count.groups.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_count_groups" name="Count.groups" version="1.23.0" > <description>counts the number of sequences represented by a specific group or set of groups</description> <command interpreter="python"> mothur_wrapper.py --cmd='count.groups' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.groups.count$:'$grp_count,'^\S+\.summary$: '$summary --outputdir='$logfile.extra_files_path' #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): --shared=$group #elif isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('count_table').__class__): --count=$group #else: --group=$group #end if #if $groupnames.source == 'groups': #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0: --groups=$groupnames.groups #end if #elif $groupnames.source == 'accnos': #if $groupnames.accnos.__str__ != "None" and len($groupnames.accnos.__str__) > 0: --accnos=$groupnames.accnos #end if #end if </command> <inputs> <param name="group" type="data" format="groups,shared,count_table" label="group, shared, or count_table - Group file for sequence count"/> <conditional name="groupnames"> <param name="source" type="select" label="Filter group names"> <option value="none">Report on All Groups</option> <option value="groups">A List of Group Names</option> <option value="accnos">A History Group Name Accnos Dataset</option> </param> <when value="none"/> <when value="groups"> <param name="groups" type="select" label="groups - Pick groups to include" multiple="true"> <help>All groups displayed if none are selected.</help> <options> <filter type="data_meta" ref="group" key="groups" /> </options> </param> </when> <when value="accnos"> <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Group Names from your history"/> </when> </conditional> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="grp_count" label="${tool.name} on ${on_string}: group.count" /> <data format="tabular" name="summary" label="${tool.name} on ${on_string}: 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 count.groups_ command counts sequences from a specific group or set of groups from a group_ or shared_ file. .. _shared: http://www.mothur.org/wiki/Shared_file .. _group: http://www.mothur.org/wiki/Group_file .. _count.groups: http://www.mothur.org/wiki/Count.groups </help> </tool>