Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/get.otus.xml @ 12:370b3fc4e7d3
Mothur galaxy tool updates for Mothur version 1.21.0, fix help section warnings
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 09 Aug 2011 11:39:27 -0500 |
parents | e990ac8a0f58 |
children | bfbaf823be4c |
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<tool id="mothur_get_otus" name="Get.otus" version="1.19.0"> <description>Get otus containing sequences from specified groups</description> <command interpreter="python"> mothur_wrapper.py ## output {group_file_name}.pick.{label}.groups {list_file_name}.pick.{label}.list #import re, os.path --cmd='get.otus' --outputdir='$logfile.extra_files_path' --group=$group_in --list=$list_in --label=$label #if $groupnames.source == 'groups': #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0: --groups=$groupnames.groups #end if #else #if $groupnames.accnos.__str__ != "None" and len($groupnames.accnos.__str__) > 0: --accnos=$groupnames.accnos #end if #end if #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] #set results = $results + ["'" + $re.sub(r'^(.*)\.(.*?)',r'\1.pick.' + $label.__str__ + r'.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] #set results = $results + ["'" + $re.sub(r'^(.*)\.(.*?)',r'\1.pick.'+ $label.__str__ + r'.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] --result=#echo ','.join($results) </command> <inputs> <param name="group_in" type="data" format="groups" label="group - Groups"/> <param name="list_in" type="data" format="list" label="list - OTU List"/> <param name="label" type="select" label="label - OTU Labels" > <options from_dataset="list_in"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> <conditional name="groupnames"> <param name="source" type="select" label="Select Group Names from"> <option value="groups">A List of Group Names</option> <option value="accnos">A History Group Name Accnos Dataset</option> </param> <when value="groups"> <param name="groups" type="select" label="groups - Pick groups to include" multiple="true" force_select="true"> <help>At least one group must be selected</help> <options from_dataset="group_in"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="unique_value" name="unq_grp" column="1" /> </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 ${on_string}: logfile" /> <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/> </outputs> <requirements> <requirement type="binary">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.otus_ command selects otus from a list_ containing sequences from a specific group or set of groups. .. _list: http://www.mothur.org/wiki/List_file .. _get.otus: http://www.mothur.org/wiki/Get.otus </help> </tool>