<tool id="mothur_fastq_info" name="Fastq.info" version="1.25.0">
 <description>Convert fastq to fasta and quality</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='fastq.info'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fasta$:'$out_fasta,'^\S+\.qual$:'$out_qfile
  --outputdir='$logfile.extra_files_path'
  --fastq=$fastq
  --pacbio=$pacbio
  --format=$format

  #if $oligo.add == "yes":
   --oligos=$oligo.oligos
   #if $oligo.bdiffs.__str__ != '' and int($oligo.bdiffs.__str__) > 0:
    --bdiffs=$oligo.bdiffs
   #end if
   #if $oligo.pdiffs.__str__ != '' and int($oligo.pdiffs.__str__) > 0:
    --pdiffs=$oligo.pdiffs
   #end if
   #if $oligo.tdiffs.__str__ != '' and int($oligo.tdiffs.__str__) > 0:
    --tdiffs=$oligo.tdiffs
   #end if
   #if $oligo.ldiffs.__str__ != '' and int($oligo.ldiffs.__str__) > 0:
    --ldiffs=$oligo.ldiffs
   #end if
   #if $oligo.sdiffs.__str__ != '' and int($oligo.sdiffs.__str__) > 0:
    --sdiffs=$oligo.sdiffs
   #end if
   --datasetid='$fastq.info.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.(\S+\.flow)$:sff.flow'
  #end if

 </command>
 <inputs>
  <param name="fastq" type="data" format="fastq" label="fastq - Fastq Sequence file"/>
  <param name="fasta" type="boolean" truevalue="" falsevalue="--fasta=false" checked="true" label="fasta - Add fasta to your history" />
  <param name="qfile" type="boolean" truevalue="" falsevalue="--qfile=false" checked="true" label="qfile - Add qfile to your history" />

  <param name="pacbio" type="boolean" truevalue="true" falsevalue="false" checked="false" label="pacbio - if set to true, quality scores of 0 will results in a corresponding base of N" />
  <param name="format" type="select" value="sanger" label="format of sequence" >
    <option value="sanger">sanger</option>
    <option value="solexa">solexa</option>
    <option value="illumina">illumina</option>
    <option value="illumina1.8+">illumina1.8+</option>
  </param>

  <conditional name="oligo">
   <param name="add" type="select" label="Use oligos file?" 
    help="a file that contain the sequences of the forward and reverse primers and barcodes and their sample identifier.
         Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, 
         and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file.  ">
    <option value="no">no</option>
    <option value="yes">yes</option>
   </param>
   <when value="no"/>
   <when value="yes">
    <param name="oligos" type="data" format="oligos" label="oligos - barcodes and primers"/>
    <param name="bdiffs" type="integer" value="0" label="bdiffs - number of differences to allow in the barcode (default 0)">
      <validator type="in_range" message="Number of differences can't be negative" min="0"/>
    </param>
    <param name="pdiffs" type="integer" value="0" label="pdiffs - number of differences to allow in the primer (default 0)">
      <validator type="in_range" message="Number of differences can't be negative" min="0"/>
    </param>
    <param name="tdiffs" type="integer" value="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)">
      <validator type="in_range" message="Number of differences can't be negative" min="0"/>
    </param>
    <param name="ldiffs" type="integer" value="0" optional="true" label="ldiffs - total number of differences to allow in linker sequence (default 0)">
      <validator type="in_range" message="Number of differences can't be negative" min="0"/>
    </param>
    <param name="sdiffs" type="integer" value="0" optional="true" label="sdiffs - total number of differences to allow in spacer sequence (default 0)">
      <validator type="in_range" message="Number of differences can't be negative" min="0"/>
    </param>
   </when>
  </conditional>


 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta">
   <filter>fasta == True</filter>
  </data>
  <data format="qual454" name="out_qfile" label="${tool.name} on ${on_string}: qual">
   <filter>qfile == True</filter>
  </data>
 </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 fastq.info_ command reads a fastq file and creates a fasta and quality file.


.. _fastq.info: http://www.mothur.org/wiki/Fastq.info

 </help>
</tool>