comparison mothur/tools/mothur/parse.list.xml @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

1:fcc0778f6987

<tool id="mothur_parse_list" name="Parse.list" version="1.16.0" force_history_refresh="True">
 <description>Order Sequences by OTU</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='parse.list'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'

  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="list" label="list - OTU List"/>
  <param name="group" type="data" format="groups" label="group - Sequences Name reference"/>
  <param name="label" type="select" optional="true" label="label - Select OTU Labels to filter out all but selected labels" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
   </options>
  </param>

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The parse.list_ command prints out a fasta-formatted file where sequences are ordered according to the OTU that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.

.. _parse.list: http://www.mothur.org/wiki/Parse.list

 </help>
</tool>

2:e990ac8a0f58

<tool id="mothur_parse_list" name="Parse.list" version="1.19.0" force_history_refresh="True">
 <description>Generate a List file for each group</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='parse.list'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'

  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="list" label="list - OTU List"/>
  <param name="group" type="data" format="groups" label="group - Sequences Name reference"/>
  <param name="label" type="select" optional="true" label="label - To filter: Select OTU Labels to include" multiple="true">
   <help>All labels are included if none are selected</help>
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
   </options>
  </param>

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The parse.list_ command reads a list_ file and group_ file and generates a list_ file for each group_ in the groupfile.

.. _list: http://www.mothur.org/wiki/List_file
.. _group: http://www.mothur.org/wiki/Group_file
.. _parse.list: http://www.mothur.org/wiki/Parse.list

 </help>
</tool>