Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/shhh.seqs.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_shhh_seqs" name="Shhh.seqs" version="1.23.0"> <description>Denoise program (Quince SeqNoise)</description> <command interpreter="python"> mothur_wrapper.py #import re, os.path --cmd='shhh.seqs' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shhh_seqs\.fasta$:'$shhh_fasta,'^\S+\.shhh_seqs\.names$:'$shhh_names,'^\S+\.shhh\.\S+\.map$:'$shhh_map --outputdir='$logfile.extra_files_path' --fasta=$fasta --name=$name #if $group.__str__ != "None" and len($group.__str__) > 0: --group=$group #end if #if $sigma.__str__ != '': --sigma=$sigma #end if --processors=8 </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/> <param name="name" type="data" format="names" label="name - Sequences Name reference"/> <param name="group" type="data" format="groups" optional="true" label="group - Sequences Name reference"/> <param name="sigma" type="float" value="" optional="true" label="sigma" help="default .01"> <validator type="in_range" message="sigma between 0. and 1." min="0.0" max="1.0"/> </param> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="fasta" name="shhh_fasta" label="${tool.name} on ${on_string}: shhh.fasta"/> <data format="names" name="shhh_names" label="${tool.name} on ${on_string}: shhh.names"/> <data format="txt" name="shhh_map" label="${tool.name} on ${on_string}: shhh.map"/> </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 shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise. Schloss prefers pre.cluster for this operation. .. _shhh.seqs: http://www.mothur.org/wiki/Shhh.seqs </help> </tool>