comparison mothur/tools/mothur/get.seqs.xml @ 2:e990ac8a0f58

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

1:fcc0778f6987

<tool id="mothur_get_seqs" name="Get.seqs" version="1.16.0">
 <description>Picks sequences by name</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]

  <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
  <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <param name="group_in" type="data" format="groups" optional="true" label="group - Sequences Groups"/>
  <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/>
  <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/>
  <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy"/>
  <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <!-- format should be set to match input -->

   <filter>alignreport_in != None</filter>
  </data>
  <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list">
   <filter>list_in != None</filter>
  </data>
  <data format="taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy">
   <filter>taxonomy_in != None</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="binary">mothur</requirement>

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

**Command Documenation**

The get.seqs_ command takes a list of sequence names and either a fasta, name, group, list, or align.report file to generate a new file that contains only the sequences in the list. This command may be used in conjunction with the list.seqs command to help screen a sequence collection.

.. _get.seqs: http://www.mothur.org/wiki/Get.seqs


 </help>
</tool>

2:e990ac8a0f58

<tool id="mothur_get_seqs" name="Get.seqs" version="1.19.0">
 <description>Picks sequences by name</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]

  <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
  <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <param name="group_in" type="data" format="groups" optional="true" label="group - Sequences Groups"/>
  <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/>
  <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/>
  <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
  <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <!-- format should be set to match input -->

   <filter>alignreport_in != None</filter>
  </data>
  <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list">
   <filter>list_in != None</filter>
  </data>
  <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy">
   <filter>taxonomy_in != None</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="binary">mothur</requirement>

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

**Command Documenation**

The get.seqs_ command takes a list of sequence names and either a fasta, name_, group_, list_, align.report_ or taxonomy_ file to generate a new file that contains only the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection.

.. _name: http://www.mothur.org/wiki/Name_file
.. _group: http://www.mothur.org/wiki/Group_file
.. _list: http://www.mothur.org/wiki/List_file
.. _align.report: http://www.mothur.org/wiki/Align.seqs
.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
.. _list.seqs: http://www.mothur.org/wiki/list.seqs
.. _get.seqs: http://www.mothur.org/wiki/Get.seqs


 </help>
</tool>