comparison mothur/tools/mothur/remove.lineage.xml @ 12:370b3fc4e7d3

Mothur galaxy tool updates for Mothur version 1.21.0, fix help section warnings

11:11867a45a43d

  --result=#echo ','.join($results)
 </command>
 <inputs>
  <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/>
  <!--
  <param name="taxons" type="select" size="120" multiple="True" label="Browse Taxons from Taxonomy">
   <options from_dataset="taxonomy">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="unique_value" name="unique_taxon" column="1" />
   </options>
  </param>
  -->
  <param name="taxon" type="text" area="True" size="5x120" label="taxon - Select Taxons for filtering" help="Enter 1 or more taxons separated by whitespace or commas"/>
  <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>

  <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/>
  <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicate names"/>
 </inputs>
 <outputs>
  <!-- fix format -->
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/>
  <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
   <filter>fasta_in != None</filter>
  </data>

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

**Command Documenation**

The remove.lineage_ command reads a taxonomy_ file and a taxon and generates a new file that contains only the sequences in the that are not from that taxon. You may also include either a fasta_, name_, group_, list_, or align.report_ file to this command and mothur will generate new files for each of those containing only the selected sequences.

.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
.. _name: http://www.mothur.org/wiki/Name_file
.. _group: http://www.mothur.org/wiki/Group_file
.. _list: http://www.mothur.org/wiki/List_file

12:370b3fc4e7d3

  --result=#echo ','.join($results)
 </command>
 <inputs>
  <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/>
  <!--
  <param name="taxons" type="select" size="120" multiple="true" label="Browse Taxons from Taxonomy">
   <options from_dataset="taxonomy">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="unique_value" name="unique_taxon" column="1" />
    <filter type="sort_by" name="sorted_taxon" column="1" />
   </options>
  </param>
  -->
  <param name="taxon" type="text" area="True" size="5x120" label="taxon - Select Taxons for filtering" help="Enter 1 or more taxons separated by whitespace or commas"/>
  <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>

  <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/>
  <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicate names"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/>
  <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
   <filter>fasta_in != None</filter>
  </data>

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

**Command Documenation**

The remove.lineage_ command reads a taxonomy_ file and a taxon and generates a new file that contains only the sequences in the that are not from that taxon. You may also include either a fasta, name_, group_, list_, or align.report_ file to this command and mothur will generate new files for each of those containing only the selected sequences.

.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
.. _name: http://www.mothur.org/wiki/Name_file
.. _group: http://www.mothur.org/wiki/Group_file
.. _list: http://www.mothur.org/wiki/List_file