Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/make.contigs.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
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Wed, 04 Sep 2013 10:51:34 -0500 |
parents | a3eed59297ea |
children | 95d75b35e4d2 |
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<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 "forward", "reverse", and "barcode" or it can start with a "#" 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>