annotate mothur/tools/mothur/list.seqs.xml @ 36:040410b8167e default tip

Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.

<tool id="mothur_list_seqs" name="List.seqs" version="1.20.0">
 <description>Lists the names (accnos) of the sequences</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='list.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.accnos$:'$out_file
  --outputdir='$logfile.extra_files_path'
  #if $search.type == "fasta":
   --fasta=$search.input
  #elif $search.type == "name":
   --name=$search.input
  #else if $search.type == "group":
   --group=$search.input
  #elif $search.type == "alignreport":
   --alignreport=$search.input
  #elif $search.type == "list":
   --list=$search.input
  #elif $search.type == "taxonomy":
   --taxonomy=$search.input
  #end if
	#if $count.__str__ != "None" and len($count.__str__) > 0:
		--count=$count
	#end if
 </command>
 <inputs>
  <conditional name="search">
   <param name="type" type="select" label="Type to list" help="">
    <option value="fasta">Sequence Fasta</option>
    <option value="name">Sequences Name reference</option>
    <option value="group">Groups</option>
    <option value="alignreport">Align Report</option>
    <option value="list">OTU List</option>
    <option value="taxonomy">Sequence Taxonomy</option>
   </param>
   <when value="fasta">
    <param name="input" type="data" format="fasta" label="fasta - Fasta"/>
   </when>
   <when value="name">
    <param name="input" type="data" format="names" label="name - Names"/>
   </when>
   <when value="group">
    <param name="input" type="data" format="groups" label="group - Groups"/>
   </when>
   <when value="alignreport">
    <param name="input" type="data" format="align.report" label="alignreport - Align Report"/>
   </when>
   <when value="list">
    <param name="input" type="data" format="list" label="list - OTU List"/>
   </when>
   <when value="taxonomy">
    <param name="input" type="data" format="seq.taxonomy" label="taxonomy - Sequence Taxonomy"/>
   </when>
  </conditional>
	<param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
	<param name="count" type="data" format="fastq" optional="true" label="fastq"/>
 </inputs>
 <outputs>
  <!-- fix format -->
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="accnos" name="out_file" label="${tool.name} on ${on_string}: accnos" />
 </outputs>
 <requirements>
<requirement type = "package" version ="1.33">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 list.seqs_ command writes out the names of the sequences found within a fasta, name_, group_, list_, align.report_ or taxonomy_ file.

.. _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

v.1.20.0: Updated to mothur 1.33, added count and fastq option

 </help>
</tool>