Mercurial > repos > jjohnson > mothur_toolsuite
diff mothur/tools/mothur/make.shared.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | |
children | 11867a45a43d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/make.shared.xml Tue Jun 07 17:39:06 2011 -0400 @@ -0,0 +1,75 @@ +<tool id="mothur_make_shared" name="Make.shared" version="1.19.0" force_history_refresh="True"> + <description>Make a shared file from a list and a group</description> + <command interpreter="python"> + mothur_wrapper.py + #import re, os.path + --cmd='make.shared' + --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared$:'$shared + --outputdir='$logfile.extra_files_path' + #if $as_datasets.__str__ == "yes": + --datasetid='$logfile.id' --new_file_path='$__new_file_path__' + --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund' + #end if + --list=$list + --group=$group + #if $label.__str__ != "None" and len($label.__str__) > 0: + --label='$label' + #end if + #if $groups.__str__ != "None" and len($groups.__str__) > 0: + --unique=$groups + #end if + #if $ordergroup.__str__ != "None" and len($ordergroup.__str__) > 0: + --ordergroup=$ordergroup + #end if + </command> + <inputs> + <param name="list" type="data" format="list" label="list - OTU List"/> + <param name="group" type="data" format="groups" label="group - "/> + <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" + help="By default all are included if no selection is made."> + <options from_dataset="list"> + <column name="name" index="0"/> + <column name="value" index="0"/> + </options> + </param> + <param name="groups" type="select" label="groups - Groups to include" multiple="true"> + <options from_dataset="group"> + <column name="name" index="1"/> + <column name="value" index="1"/> + <filter type="unique_value" name="unq_grp" column="1" /> + </options> + </param> + <param name="ordergroup" type="data" format="groups" optional="true" label="ordergroup - one column list of group names in desired order"/> + <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each group rabund"/> + </inputs> + <outputs> + <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> + <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" /> + </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 make.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group. + + +.. _list: http://www.mothur.org/wiki/List_file +.. _group: http://www.mothur.org/wiki/Group_file +.. _shared: http://www.mothur.org/wiki/Shared_file +.. _rabund: http://www.mothur.org/wiki/Rabund_file +.. _make.shared: http://www.mothur.org/wiki/Make.shared + + </help> +</tool>