annotate mothur/tools/mothur/make.contigs.xml @ 31:a3eed59297ea

Patches courtesy of Peter Briggs, Bioinformatics Core Facility University of Manchester make.contigs.xml.patch:# make.contigs.xml.patch make.contigs.xml.patch:# make.contigs.xml.patch:# 1. Fix cosmetic typo in <description> (forard -> forward) make.contigs.xml.patch:# 2. Address error due to having 'mismatch' as the name for both an input and an output parameter: make.contigs.xml.patch:# rename output parameter to 'cmismatch' make.contigs.xml.patch:# 3. Remove 'threshold' parameter: make.contigs in mothur doesn't support a 'threshold' parameter metagenomics.py.patch:# metagenomics.py.patch metagenomics.py.patch:# metagenomics.py.patch:# 1. Groups class: names were being taken from the wrong field (affected shhh.flows tool) metagenomics.py.patch:# 2. Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular metagenomics.py.patch:# data uploads being sniffed as this type mothur_wrapper.py.patch:# mothur_wrapper.py.patch mothur_wrapper.py.patch:# mothur_wrapper.py.patch:# 1. Update 'cmd_dict' settings for shhh.flows and shhh.seqs (otherwise these functions will mothur_wrapper.py.patch:# fail on execution) mothur_wrapper.py.patch:# 2. Fix add_option calls defining '--match' and '--mismatch' command line options (otherwise mothur_wrapper.py.patch:# syntax error causes immediate failure) screen.seqs.xml.patch:# screen.seqs.xml.patch screen.seqs.xml.patch:# screen.seqs.xml.patch:# Replace pattern for align.report output file in definiting of 'results' parameter in screen.seqs.xml.patch:# <command> section (otherwise output_alignreport data item is empty). shhh.flows.xml.patch:# shhh.flows.xml.patch shhh.flows.xml.patch:# shhh.flows.xml.patch:# Replace 'format_source' with 'format' for output parameters (otherwise formats are not shhh.flows.xml.patch:# correctly assigned to output datasets) shhh.seqs.xml.patch:# shhh.seqs.xml.patch shhh.seqs.xml.patch:# shhh.seqs.xml.patch:# 1. Fix patterns in --result (in <command> section) for shhh_seqs.fasta and shhh_seqs.names shhh.seqs.xml.patch:# output files (otherwise files are not collected and associated data items are empty) shhh.seqs.xml.patch:# 2. Replace 'format_source' with 'format' for output parameters (otherwise formats are not shhh.seqs.xml.patch:# correctly assigned to output datasets) trim.flows.xml.patch:# trim.flows.xml.patch trim.flows.xml.patch:# trim.flows.xml.patch:# Remove erroneous space from --result definition in <command> section (otherwise causes tool trim.flows.xml.patch:# failure) trim.seqs.xml.patch:# trim.seqs.xml.patch trim.seqs.xml.patch:# trim.seqs.xml.patch:# 1. Remove reference to undefined 'oligo.allvalues' varible in <command> section (otherwise trim.seqs.xml.patch:# causes failure on execution) trim.seqs.xml.patch:# 2. Fix format for input parameter 'names' (format should be 'names' not 'name') trim.seqs.xml.patch:# 3. Add output parameter 'scrap_names' (to ensure consistent collection of all outputs) trim.seqs.xml.patch:# 4. Update --result definition in <command> section to collect both trim.names and scrap.names

<tool id="mothur_make_contigs" name="Make.contigs" version="1.26.0">
 <description>Aligns paired forward and reverse fastq files to contigs as fasta and quality</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='make.contigs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.contigs\.fasta$:'$fasta,'^\S+\.contigs\.qual$:'$qual,'^\S+\.contigs\.mismatch$:'$cmismatch
  --outputdir='$logfile.extra_files_path'
  --ffastq=$ffastq
  --rfastq=$rfastq
  --align=$align
  #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
  #end if

  #if $match.__str__ != '':
   --match=$match
  #end if
  #if $mismatch.__str__ != '':
   --mismatch=$mismatch
  #end if
  #if $gapopen.__str__ != '':
   --gapopen=$gapopen
  #end if
  #if $gapextend.__str__ != '':
   --gapextend=$gapextend
  #end if
  ###if $threshold.__str__ != '':
  ## --threshold=$threshold
  ###end if
  --processors=8
 </command>
 <inputs>
  <param name="ffastq" type="data" format="fastq" label="ffastq - Forward Fastq Sequence file"/>
  <param name="rfastq" type="data" format="fastq" label="rfastq - Reverse Fastq Sequence file"/>
  <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
   <option value="gotoh" selected="true">gotoh (default)</option>
   <option value="needleman">needleman</option>
  </param>
  <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" optional="true" label="oligos - barcodes and primers"
           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.  "/>
    <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>
   </when>
  </conditional>
  <param name="match" type="integer" value="1" optional="true" label="match - Pairwise alignment reward for a match"/>
  <param name="mismatch" type="integer" value="-1" optional="true" label="mismatch - Pairwise alignment penalty for a mismatch"/>
  <param name="gapopen" type="integer" value="-2" optional="true" label="gapopen - Pairwise alignment penalty for opening a gap"/>
  <param name="gapextend" type="integer" value="-1" optional="true" label="gapextend - Pairwise alignment penalty for extending a gap"/>
  <!-- make.contigs doesn't support "threshold" option, see http://www.mothur.org/wiki/Make.contigs
  <param name="threshold" type="integer" value="40" optional="true" label="threshold - for quality scores" 
         help="When we are merging the overlapping regions, in the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score below the threshold we eliminate it.">
      <validator type="in_range" message="threshold can't be negative" min="0"/>
  </param>
  -->
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="fasta" name="fasta" label="${tool.name} on ${on_string}: contigs.fasta"/>
  <data format="qual" name="qual" label="${tool.name} on ${on_string}: contigs.qual"/>
  <data format="txt" name="cmismatch" label="${tool.name} on ${on_string}: contigs.mismatch"/>
 </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 make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.

.. _make.contigs: http://www.mothur.org/wiki/Make.contigs

 </help>
</tool>