<tool id="mothur_sort_seqs" name="Sort.seqs" version="1.24.0">
 <description>put sequences in different files in the same order</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  ## adds .sorted before the last extension to the input file (except group has .pick) 
  --cmd='sort.seqs'
  --outputdir='$logfile.extra_files_path'
  #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0:
   --fasta=$fasta_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.sorted.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__]
  #end if
  #if $qfile_in.__str__ != "None" and len($qfile_in.__str__) > 0:
   --qfile=$qfile_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.sorted.\2',$os.path.basename($qfile_in.__str__)) + ":'" + $qfile_out.__str__]
  #end if
  #if $flow_in.__str__ != "None" and len($flow_in.__str__) > 0:
   --flow=$flow_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.sorted.\2',$os.path.basename($flow_in.__str__)) + ":'" + $flow_out.__str__]
  #end if
  #if $name_in.__str__ != "None" and len($name_in.__str__) > 0:
   --name=$name_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.sorted.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__]
  #end if
  #if $group_in.__str__ != "None" and len($group_in.__str__) > 0:
   --group=$group_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__]
  #end if
  #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0:
   --taxonomy=$taxonomy_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.sorted.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__]
  #end if
  #if $accnos.__str__ != "None" and len($accnos.__str__) > 0:
   --accnos=$accnos
  #end if
  $large
  --result=#echo ','.join($results)
 </command>
 <inputs>
  <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences"/>
  <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - sequence quality"/>
  <param name="flow_in" type="data" format="sff.flow" optional="true" label="flow - sff flowgram "/>
  <param name="group_in" type="data" format="groups" optional="true" label="groups - sequence groupings"/>
  <param name="name_in" type="data" format="names" optional="true" label="names - name reference"/>
  <param name="taxonomy_in" type="select" format="seq.taxonomy" optional="true" label="taxonomy - taxonomy reference"/>
  <param name="accnos" type="data" format="accnos" optional="true" label="accnos - sort "/>
  <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Datasets are large and may not fit in RAM"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: sorted.fasta">
    <filter>fasta_in != None</filter>
  </data>
  <data format_source="qfile_in" name="qfile_out" label="${tool.name} on ${on_string}: sorted.qfile">
    <filter>qfile_in != None</filter>
  </data>
  <data format_source="flow_in" name="flow_out" label="${tool.name} on ${on_string}: sorted.flow">
    <filter>flow_in != None</filter>
  </data>
  <data format_source="group_in" name="group_out" label="${tool.name} on ${on_string}: sorted.group">
    <filter>group_in != None</filter>
  </data>
  <data format_source="name_in" name="name_out" label="${tool.name} on ${on_string}: sorted.name">
    <filter>name_in != None</filter>
  </data>
  <data format_source="taxonomy_in" name="taxonomy_out" label="${tool.name} on ${on_string}: sorted.taxonomy">
    <filter>taxonomy_in != None</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">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 sort.seqs_ command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order.
You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads.

.. _sort.seqs: http://www.mothur.org/wiki/Sort.seqs


 </help>
</tool>