annotate mothur/tools/mothur/trim.flows.xml @ 32:ec8df51e841a

Fixes courtesy of Peter Briggs: metagenomics.py: - Groups class: Fix for when second column not present - Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular data uploads being sniffed as this type mothur_wrapper.py: - update cmd_dict['chimera.perseus'], to use correct inputs - add --beta option (needed for chimera.perseus tool) - add function for converting input floats from scientific notation (e.g. 1e-6, which mothur can't handle) to decimal format (e.g. 0.00001, which it can) chimera.perseus.xml: - add output data item for the "accnos" file (not previous captured in the history) trim.flows.xml: - cosmetic change: base name for additional output data items is now "trim.flows", rather than "logfile" (clarifies history items) shhh.flows.xml: - cosmetic change: update default value specified in help for mindiff to be consistent with that given in the mothur documentation

<tool id="mothur_trim_flows" name="Trim.flows" version="1.22.0" force_history_refresh="True">
 <description>partition by barcode, trim to length, cull by lenght and mismatches</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='trim.flows'
  ## #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  ## #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($flow.__str__)) + ":'" + $trim_flow.__str__]
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.trim\.flow$:'$trim_flow,'^\S+\.scrap\.flow$:'$scrap_flow,'^\S+\.flow\.files$:'$flow_files,'^\S+\.flow\.fasta$:'$flow_fasta
  --outputdir='$logfile.extra_files_path'
  --flow=$flow
  #if $minflows.__str__ != '':
   --minflows=$minflows 
  #end if
  #if $maxflows.__str__ != '':
   --maxflows=$maxflows 
  #end if
  #if $maxhomop.__str__ != '':
   --maxhomop=$maxhomop 
  #end if
  #if $order.__str__.strip() != '':
   --order=$order 
  #end if
  #if $signal.__str__ != ''
   --signal=$signal 
  #end if
  #if $noise.__str__ != ''
   --noise=$noise 
  #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=$oligo.sdiffs
   #end if
   --datasetid='$trim_flow.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.(\S+\.flow)$:sff.flow'
  #end if
  $fasta
  --processors=8
 </command>
 <inputs>
  <param name="flow" type="data" format="sff.flow" label="flow - flowgram data" 
         help="Use sffinfo to generate flow data from an sff file"/>

  <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="minflows" type="integer" value="" optional="true" label="minflows - Minimum number of flows that each sequence must contain to make it in to a &quot;trim&quot; file. (default 450)" help="(Quince uses 360)"/>
  <param name="maxflows" type="integer" value="" optional="true" label="maxflows - Maximum number of flows after which all other flows should be ignored (default 450)" help="(Quince uses 360 for GSFLX and 720 for Titanium)"/>

  <param name="maxhomop" type="integer" value="" optional="true" label="maxhomop - Maximum homopolymers" 
         help=""/>

  <param name="signal" type="float" value="" optional="true" label="signal - treat any intensity signal greater than this threshold as a real signal" 
         help="default .5">
   <validator type="in_range" message="signal between 0. and 1." min="0.0" max="1.0"/>
  </param>
  <param name="noise" type="float" value="" optional="true" label="noise - treat any intensity signal less than this threshold as noise" 
         help="default .7">
   <validator type="in_range" message="signal between 0. and 1." min="0.0" max="1.0"/>
  </param>
  <param name="order" type="text" value="" label="order - flow order for nucleotides in the sequencer" 
         help="default is TACG"/>

  <param name="fasta" type="boolean" truevalue="--fasta=true" falsevalue="" checked="false" label="fasta - translate the flowgram data to fasta sequence format"/>

 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="sff.flow" name="trim_flow" label="${tool.name} on ${on_string}: trim.flow"/>
  <data format="sff.flow" name="scrap_flow" label="${tool.name} on ${on_string}: scrap.flow"/>
  <data format="tabular" name="flow_files" label="${tool.name} on ${on_string}: flow.files">
   <filter>oligos != None</filter>
  </data>
  <data format_source="fasta" name="flow_fasta" label="${tool.name} on ${on_string}: flow.fasta">
   <filter>fasta == True</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 trim.flows_ command is analogous to the trim.seqs command, except that it uses the flowgram data that comes bundled in the sff file that is generated by 454 sequencing. It's primary usage is as a preliminary step to running shhh.seqs. Chris Quince has a series of perl scripts that fulfill a similar role [1]. This command will allow you to partition your flowgram data by sample based on the barcode, trim the flows to a specified length range, and cull sequences that are too short or have too many mismatches to barcodes and primers.

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


 </help>
</tool>