Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/align.seqs.xml @ 1:fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:35:35 -0400 |
parents | 3202a38e44d9 |
children | e990ac8a0f58 |
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<tool id="mothur_align_seqs" name="Align.seqs" version="1.16.0"> <description>Align sequences to a template alignment</description> <command interpreter="python"> mothur_wrapper.py --cmd='align.seqs' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align$:'$out_file,'^\S+\.align\.report$:'$report --outputdir='$logfile.extra_files_path' --candidate=$candidate --template=$alignment.template #if $search.method == 'kmer': --ksize=$search.ksize #else: --search=$search.method #end if --align=$align #if $scoring.adjust == 'yes': --match=$scoring.match --mismatch=$scoring.mismatch --gapopen=$scoring.gapopen --gapextend=$scoring.gapextend #end if #if $reverse.flip == 'yes': --flip=true --threshold=$reverse.threshold #end if --processors=2 </command> <inputs> <param name="candidate" type="data" format="fasta" label="candidate - Candiate Sequences"/> <conditional name="alignment"> <param name="source" type="select" label="Select Template from" help=""> <option value="hist">History</option> <option value="ref">Cached Reference</option> </param> <when value="ref"> <param name="template" type="select" label="template - Select an alignment database " help=""> <options from_file="mothur_aligndb.loc"> <column name="name" index="0" /> <column name="value" index="1" /> </options> </param> </when> <when value="hist"> <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/> </when> </conditional> <conditional name="search"> <param name="method" type="select" label="Select a search method" help=""> <option value="kmer">kmer (default)</option> <option value="suffix">suffix tree</option> <option value="blast">blast</option> </param> <when value="kmer"> <param name="ksize" type="integer" value="8" label="ksize - kmer length between 5 and 12"> <validator type="in_range" message="ksize - kmer length between 5 and 12" min="5" max="12"/> </param> </when> <when value="suffix"/> <when value="blast"/> </conditional> <param name="align" type="select" label="align - Select a pairwise alignment method" help=""> <option value="needleman">needleman (default)</option> <option value="gotoh">gotoh</option> <option value="blast">blast</option> </param> <conditional name="scoring"> <param name="adjust" type="select" label="Alignment scoring values" help=""> <option value="no">use defaults</option> <option value="yes">adjust values</option> </param> <when value="no"/> <when value="yes"> <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/> <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/> <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/> <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/> </when> </conditional> <conditional name="reverse"> <param name="flip" type="select" label="flip - Try to align against the reverse complement" help=""> <option value="no">No</option> <option value="yes">Yes values</option> </param> <when value="no"/> <when value="yes"> <param name="threshold" type="float" value=".5" label="threshold - Cutoff (0. - 1.) at which an alignment is deemed 'bad' and the reverse complement may be tried."/> </when> </conditional> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="align" name="out_file" label="${tool.name} on ${on_string}: align" /> <data format="align.report" name="report" label="${tool.name} on ${on_string}: align.report" /> </outputs> <requirements> <requirement type="binary">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 align.seqs_ command aligns a user-supplied fasta-formatted candidate sequence file to a user-supplied fasta-formatted template alignment. .. _align.seqs: http://www.mothur.org/wiki/Align.seqs </help> </tool>