Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/pcr.seqs.xml @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author | certain cat |
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date | Fri, 31 Oct 2014 15:09:32 -0400 |
parents | 49058b1f8d3f |
children | 040410b8167e |
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<tool id="mothur_pcr_seqs" name="Pcr.seqs" version="1.26.0"> <description>Trim sequences</description> <command interpreter="python"> mothur_wrapper.py --cmd='pcr.seqs' #import re, os.path #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] ## adds .pcr before the last extension to the input file #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pcr.\2',$os.path.basename($fasta.__str__)) + ":'" + $pcr_fasta.__str__] #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pcr.scrap.\2',$os.path.basename($fasta.__str__)) + ":'" + $scrap_fasta.__str__] --outputdir='$logfile.extra_files_path' --fasta=$fasta #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: --name=$name_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pcr.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] #end if #if $group_in.__str__ != "None" and len($group_in.__str__) > 0: --group=$group_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pcr.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] #end if #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: --taxonomy=$taxonomy_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pcr.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] #end if #if $trim.method == 'oligos': --oligos=$trim.oligos --nomatch=$trim.nomatch $trim.keepprimer #elif $trim.method == 'reference': --ecoli=$trim.ecoli #elif $trim.method == 'position': #if $trim.start.__str__ != '' and int($trim.start.__str__) > 0: --start=$trim.start #end if #if $trim.end.__str__ != '' and int($trim.end.__str__) > 0: --end=$trim.end #end if #end if $keepdots --result=#echo ','.join($results) --processors=8 #if $pdiffs.__str__ != '' and int($pdiffs.__str__) > 0: --pdiffs=$pdiffs #end if </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> <conditional name="trim"> <param name="method" type="select" label="Trim with an oligos file?" help=""> <option value="oligos">oligos</option> <option value="reference">reference sequence</option> <option value="position">start and end positions</option> </param> <when value="oligos"> <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="nomatch" type="select" label="nomatch - action when no primer is found" help=""> <option value="reject" selected="true">reject (default)</option> <option value="keep">keep</option> </param> <param name="keepprimer" type="boolean" falsevalue="" truevalue="--keepprimer=true" checked="false" label="keepprimer - keep the primer in the output sequence"/> </when> <when value="reference"> <param name="ecoli" type="data" format="fasta" optional="true" label="ecoli - An aligned reference sequence for trimming" help="The ecoli parameter is used to provide a fasta file containing a single reference sequence (e.g. for e. coli) this must be aligned. Mothur will trim to the start and end positions of the reference sequence."/> </when> <when value="position"> <param name="start" type="integer" value="" optional="true" label="start - a starting position to trim to"> <validator type="in_range" message="Starting position can't be negative" min="0"/> </param> <param name="end" type="integer" value="" optional="true" label="end - a ending position to trim from"> <validator type="in_range" message="Starting position can't be negative and should be " min="0"/> </param> </when> </conditional> <!-- trimtype --> <param name="keepdots" type="boolean" falsevalue="--keepdots=false" truevalue="" checked="true" label="keepdots - keep the leading and trailing alignment dots in the output sequences"/> <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Sequence Taxonomy"/> <param name="name_in" type="data" format="names" optional="true" label="name - Sequence representative name list"/> <param name="group_in" type="data" format="groups" optional="true" label="group - Group file"/> <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> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format_source="fasta" name="pcr_fasta" label="${tool.name} on ${on_string}: pcr.fasta" /> <data format_source="fasta" name="scrap_fasta" label="${tool.name} on ${on_string}: pcr.scrap.fasta" /> <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: tax.summary" > <filter>taxonomy_in != None</filter> </data> <data format="groups" name="group_out" label="${tool.name} on ${on_string}: " > <filter>group_in != None</filter> </data> <data format="names" name="name_out" label="${tool.name} on ${on_string}: " > <filter>name_in != None</filter> </data> </outputs> <requirements> <requirement type="package" version="1.33">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 pcr.seqs_ command assigns sequences to chosen taxonomy outline. .. _pcr.seqs: http://www.mothur.org/wiki/Pcr.seqs </help> </tool>