Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/chimera.perseus.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 | 49058b1f8d3f |
children | 95d75b35e4d2 |
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<tool id="mothur_chimera_perseus" name="Chimera.perseus" version="1.23.0" > <description>Find putative chimeras using chimeraCheck</description> <command interpreter="python"> mothur_wrapper.py --cmd='chimera.perseus' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file,'^\S+\.perseus\.accnos$:'$out_accnos --outputdir='$logfile.extra_files_path' --fasta=$fasta --name=$name #if $group.__str__ != "None" and len($group.__str__) > 0: --group='$group' #end if #if $alpha.__str__ != '': --alpha=$alpha #end if #if $beta.__str__ != '': --beta=$beta #end if #if $cutoff.__str__ != '': --cutoff=$cutoff #end if --processors=8 </command> <inputs> <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/> <param name="name" type="data" format="names" label="name - Names "/> <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/> <param name="alpha" type="float" value="-5.54" optional="true" label="alpha" help="The default is -5.54"/> <param name="beta" type="float" value="0.33" optional="true" label="beta" help="The default is 0.33"/> <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" /> <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: perseus.accnos" /> </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 chimera.perseus_ command reads a fasta and name file, and outputs potentially chimeric sequences. .. _chimera.perseus: http://www.mothur.org/wiki/Chimera.perseus </help> </tool>