Mercurial > repos > jjohnson > mothur_toolsuite
changeset 8:561fa7324f60 draft
Add make.contigs
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Fri, 30 Nov 2012 08:19:24 -0600 (2012-11-30) |
parents | 3cfe41810949 |
children | 999d1b7c7a83 |
files | mothur/tools/mothur/make.contigs.xml |
diffstat | 1 files changed, 106 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tools/mothur/make.contigs.xml Fri Nov 30 08:19:24 2012 -0600 @@ -0,0 +1,106 @@ +<tool id="mothur_make_contigs" name="Make.contigs" version="1.26.0"> + <description>Aligns paired forard 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$:'$mismatch + --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"/> + <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 ${on_string}: contigs.qual"/> + <data format="txt" name="mismatch" label="${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>