Mercurial > repos > jjohnson > mothur_toolsuite
view 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
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Tue, 30 Jul 2013 09:26:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
line wrap: on
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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>