view mothur/tools/mothur/trim.seqs.xml @ 35:95d75b35e4d2

Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)

<tool id="mothur_trim_seqs" name="Trim.seqs" version="1.25.0" force_history_refresh="True">
 <description>Trim sequences - primers, barcodes, quality</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='trim.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.trim\.fasta$:'$trim_fasta,'^\S+\.trim\.names$:'$trim_names,'^\S+\.trim\.qual$:'$trim_qual,'^\S+\.scrap\.fasta$:'$scrap_fasta,'^\S+\.scrap\.names$:'$scrap_names,'^\S+\.scrap\.qual$:'$scrap_qual,'^\S+\.groups$:'$groups_file
  --outputdir='$logfile.extra_files_path'
  #if int($minlength.__str__) > 0:
   --minlength=$minlength 
  #end if
  #if int($maxlength.__str__) > 0:
   --maxlength=$maxlength 
  #end if
  #if int($maxambig.__str__) >= 0:
   --maxambig=$maxambig 
  #end if
  #if int($maxhomop.__str__) > 0:
   --maxhomop=$maxhomop 
  #end if
  #if int($keepfirst.__str__) > 0:
   --keepfirst=$keepfirst 
  #end if
  #if int($removelast.__str__) > 0:
   --removelast=$removelast 
  #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
   $oligo.keepforward
   ##$oligo.allvalues
   #if $oligo.allfiles == True:
    --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
    --new_datasets='^\S+?\.(\S+\.fasta)$:${fasta.ext}','^\S+?\.(\S+\.groups)$:groups'
   #end if
  #end if
  #if $qual.add == "yes":
   --qfile=$qual.qfile
   #if int($qual.qaverage.__str__) > 0:
    --qaverage=$qual.qaverage
   #end if
   #if int($qual.qthreshold.__str__) > 0:
    --qthreshold=$qual.qthreshold
   #end if
   #if int($qual.qwindowaverage.__str__) > 0:
    --qwindowaverage=$qual.qwindowaverage
   #end if
   #if int($qual.qwindowsize.__str__) > 0:
    --qwindowsize=$qual.qwindowsize
   #end if
   #if int($qual.rollaverage.__str__) > 0:
    --rollaverage=$qual.rollaverage
   #end if
   #if int($qual.qstepsize.__str__) > 0:
    --qstepsize=$qual.qstepsize
   #end if
   $qual.qtrim
  #end if
  $flip 
  --fasta=$fasta
  #if $names.__str__ != "None" and len($names.__str__) > 0:
   --name=$names
  #end if

  $logtransform
  $checkorient
  #if $count.__str__ != "None" and len($count.__str__) > 0:
    --count=$count
  #end if
  --processors=8
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
  <param name="names" type="data" format="names" optional="true" label="name - Sequence representative name list"/>
  <param name="minlength" type="integer" value="0" label="minlength - Minimum Sequence Length (default 0, ignored if &#060; 1 )"/>
  <param name="maxlength" type="integer" value="0" label="maxlength - Maximum Sequence Length (default 0, ignored if &#060; 1)"/>
  <param name="maxambig" type="integer" value="-1" label="maxambig - Maximum ambiguous bases (default -1, ignored if &#060; 0)"/>
  <param name="maxhomop" type="integer" value="0" label="maxhomop - Maximum homopolymers (default 0, ignored if &#060; 1)"/>
  <param name="keepfirst" type="integer" value="0" label="keepfirst - ignored if &#060; 0)" 
         help="trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements"/>
  <param name="removelast" type="integer" value="0" label="removelast - ignored if &#060; 0)" 
         help="removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements."/>
  <conditional name="oligo">
   <param name="add" type="select" label="Trim with an oligos file?" help="">
    <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>
    <param name="keepforward" type="boolean" truevalue="--keepforward=true" falsevalue="" checked="false" label="keepforward - keep the primer"/>
    <param name="allfiles" type="boolean" truevalue="--allfiles=true" falsevalue="" checked="false" label="allfiles - separate into file per barcode"/>
   </when>
  </conditional>
  <conditional name="qual">
   <param name="add" type="select" label="Trim based on a quality file?" help="">
    <option value="no">no</option>
    <option value="yes">yes</option>
   </param>
   <when value="no"/>
   <when value="yes">
    <param name="qfile" type="data" format="qual454" label="qfile - 454 quality file"/>
    <param name="qaverage" type="integer" value="0" label="qaverage - remove sequences that have an average base quality below this value (ignored if &#060; 1)"/>
    <param name="qthreshold" type="integer" value="0" label="qthreshold - remove sequences that have any base quality below this value (ignored if &#060; 1)"/>
    <param name="qwindowaverage" type="integer" value="0" label="qwindowaverage - remove sequences that have an average base quality below this value over a window (ignored if &#060; 1)"/>
    <param name="qwindowsize" type="integer" value="50" label="qwindowsize - number of bases in a window. Default=50."/>
    <param name="rollaverage" type="integer" value="0" label="rollaverage - remove sequences that have an average base quality below this value in a rolling window (ignored if &#060; 1)"/>
    <param name="qstepsize" type="integer" value="1" label="qstepsize - number of bases to move the window over. Default=1."/>
    <param name="qtrim" type="boolean" truevalue="--qtrim=true" falsevalue="" checked="false" label="qtrim - trim sequences below qthreshold and put in trim output, else put in scrap "/>
   </when>
  </conditional>
  <param name="flip" type="boolean" truevalue="--flip=true" falsevalue="" checked="false" label="flip - reverse complement the trimmed sequences"/>


  <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" 
         help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. If you run trim.seqs with an oligos file that contains group labels, trim.seqs will create a new *.trim.count_table with the group information included. "/>
  <param name="logtransform" type="boolean" truevalue="--logtransform=true" falsevalue="" checked="false" 
         label="logtransform - allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform."/>
  <param name="checkorient" type="boolean" truevalue="--checkorient=true" falsevalue="" checked="false"
         label="checkorient - If you are running the trim.seqs command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment. "/>


 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="fasta" name="trim_fasta" label="${tool.name} on ${on_string}: trim.fasta"/>
  <data format_source="names" name="trim_names" label="${tool.name} on ${on_string}: trim.names">
   <filter>names != None</filter>
  </data>
  <data format_source="qfile" name="trim_qual" label="${tool.name} on ${on_string}: trim.qual">
   <filter>(qual['add'] == 'yes'  and len(qual['qfile'].__str__) > 0)</filter>
  </data>
  <data format_source="fasta" name="scrap_fasta" label="${tool.name} on ${on_string}: scrap.fasta"/>
  <data format_source="names" name="scrap_names" label="${tool.name} on ${on_string}: scrap.names">
   <filter>names != None</filter>
  </data>
  <data format_source="qfile" name="scrap_qual" label="${tool.name} on ${on_string}: scrap.qual">
   <filter>(qual['add'] == 'yes'  and len(qual['qfile'].__str__) > 0)</filter>
  </data>
  <data format="groups" name="groups_file" label="${tool.name} on ${on_string}: groups">
   <filter>(oligo['add'] == 'yes' and len(oligo['oligos']) > 0)</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 trim.seqs_ command provides the preprocessing features needed to screen and sort pyrosequences.  The command will enable you to trim off primer sequences and barcodes, use the barcode information to generate a group file and split a fasta file into sub-files, screen sequences based on the qual file that comes from 454 sequencers, cull sequences based on sequence length and the presence of ambiguous bases and get the reverse complement of your sequences. While this analysis is clearly geared towards pyrosequencing collections, it can also be used with traditional Sanger sequences. 

.. _trim.seqs: http://www.mothur.org/wiki/Trim.seqs


 </help>
</tool>