view mothur/tools/mothur/sffinfo.xml @ 36:040410b8167e default tip

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

<tool id="mothur_sffinfo" name="Sffinfo" version="1.25.0">
 <description>Summarize the quality of sequences</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='sffinfo'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fasta$:'$out_fasta,'^\S+\.qual$:'$out_qfile,'^\S+\.sff\.txt$:'$out_sfftxt,'^\S+\.flow$:'$out_flow
  --outputdir='$logfile.extra_files_path'
  --sff=$sff
  $fasta
  $qfile
  $sfftxt
  $flow
  $trim
  #if $accnos.__str__ != 'None' and len($accnos.__str__) > 0:
   --accnos=$accnos
  #end if

  #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=$oligo.sdiffs
   #end if
   --datasetid='$sffinfo.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.(\S+\.flow)$:sff.flow'
  #end if
 </command>
 <inputs>
  <param name="sff" type="data" format="sff" label="sff - Sff data"/>
  <!--
  <repeat name="more" title="Additional ">
   <param name="sff" type="data" format="sff" label="sff - Sff data"/>
  </repeat>
  -->
  <!--
  <param name="datasets" type="select" display="checkboxes" multiple="True" label="datasets - Choose output files for your history" help="Selected outputs will be listed as datasets in your history">
   <option value="fasta">fasta</option>
   <option value="qfile">qfile</option>
   <option value="sfftxt">sfftxt</option>
   <option value="flow">flow</option>
  </param>
  -->


  <conditional name="oligo">
   <param name="add" type="select" label="Trim with an oligos file?" 
    help="a file that can 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>



  <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="sfftxt" type="boolean" truevalue="--sfftxt=true" falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history" />
  <param name="flow" type="boolean" truevalue="--flow=true" falsevalue="--flow=false" checked="true" label="flow - Add flow to your history" />
  <param name="trim" type="boolean" truevalue="" falsevalue="--trim=false" checked="true" label="trim - Trim sequences and quality scores" />
  <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Limit output to named Accessions"/>
 </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 ${on_string}: qual">
   <filter>qfile == True</filter>
  </data>
  <data format="txt" name="out_sfftxt" label="${tool.name} on ${on_string}: sff.txt">
   <filter>sfftxt == True</filter>
  </data>
  <data format="sff.flow" name="out_flow" label="${tool.name} on ${on_string}: flowgram">
   <filter>flow == 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 sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.


.. _sffinfo: http://www.mothur.org/wiki/Sffinfo

 </help>
</tool>