Mercurial > repos > jjohnson > mothur_toolsuite
diff mothur/tools/mothur/get.groups.xml @ 12:370b3fc4e7d3
Mothur galaxy tool updates for Mothur version 1.21.0, fix help section warnings
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Tue, 09 Aug 2011 11:39:27 -0500 |
parents | 7bfe1f843858 |
children | 09740be2bc9c |
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--- a/mothur/tools/mothur/get.groups.xml Thu Jul 14 15:21:01 2011 -0500 +++ b/mothur/tools/mothur/get.groups.xml Tue Aug 09 11:39:27 2011 -0500 @@ -1,4 +1,4 @@ -<tool id="mothur_get_groups" name="Get.groups" version="1.20.0"> +<tool id="mothur_get_groups" name="Get.groups" version="1.21.0"> <description>Select groups</description> <command interpreter="python"> mothur_wrapper.py @@ -9,43 +9,61 @@ --cmd='get.groups' --outputdir='$logfile.extra_files_path' --group=$group_in - #if $groups.__str__ != "None" and len($groups.__str__) > 0: - --groups=$groups - #end if - #if $accnos.__str__ != "None" and len($accnos.__str__) > 0: - --accnos=$accnos + #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 #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: --fasta=$fasta_in - #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__] + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__] #end if #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: --name=$name_in - #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] #end if #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: --list=$list_in - #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] + #end if + #if $shared_in.__str__ != "None" and len($shared_in.__str__) > 0: + --shared=$shared_in + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.*\\.pick\\.\2',$os.path.basename($shared_in.__str__)) + ":'" + $shared_out.__str__] #end if #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: --taxonomy=$taxonomy_in - #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] #end if --result=#echo ','.join($results) </command> <inputs> <param name="group_in" type="data" format="groups" label="group - Groups"/> - <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> - <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> - <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Accession Names"/> - <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> + <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"> + <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" label="accnos - Group Names from your history"/> + </when> + </conditional> + <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/> <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> + <param name="shared_in" type="data" format="shared" optional="true" label="shared - OTU Shared"/> <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> </inputs> <outputs> @@ -61,6 +79,9 @@ <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> <filter>list_in != None</filter> </data> + <data format="shared" name="shared_out" label="${tool.name} on ${on_string}: pick.shared"> + <filter>shared_in != None</filter> + </data> <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> <filter>taxonomy_in != None</filter> </data> @@ -81,8 +102,12 @@ **Command Documenation** -The get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, name, group, list, taxonomy. +The get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, fasta, name_, group_, list_, taxonomy_. +.. _name: http://www.mothur.org/wiki/Name_file +.. _group: http://www.mothur.org/wiki/Group_file +.. _list: http://www.mothur.org/wiki/List_file +.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline .. _get.groups: http://www.mothur.org/wiki/Get.groups