Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/remove.otulabels.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_remove_otulabels" name="Remove.otulabels" version="1.26.0"> <description>Removes OTU labels</description> <command interpreter="python"> mothur_wrapper.py #import re, os.path #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] ## adds .pick before the last extension to the input file --cmd='remove.otulabels' --outputdir='$logfile.extra_files_path' --accnos=$accnos #if $constaxonomy_in.__str__ != "None" and len($constaxonomy_in.__str__) > 0: --constaxonomy=$constaxonomy_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($constaxonomy_in.__str__)) + ":'" + $constaxonomy_out.__str__] #end if #if $otucorr_in.__str__ != "None" and len($otucorr_in.__str__) > 0: --otucorr=$otucorr_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($otucorr_in.__str__)) + ":'" + $otucorr_out.__str__] #end if #if $corraxes_in.__str__ != "None" and len($corraxes_in.__str__) > 0: --corraxes=$corraxes_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($corraxes_in.__str__)) + ":'" + $corraxes_out.__str__] #end if --result=#echo ','.join($results) </command> <inputs> <param name="accnos" type="data" format="otulabels" label="accnos - otulabels"/> <param name="constaxonomy_in" type="data" format="cons.taxonomy" optional="true" label="constaxonomy - Consensus Taxonomy from classify.otu"/> <param name="otucorr_in" type="data" format="otu.corr" optional="true" label="otucorr - OTU correlation from otu.association"/> <param name="corraxes_in" type="data" format="axes" optional="true" label="corraxes - axes from corr.axes"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <!-- format should be set to match input --> <data format_source="constaxonomy_in" name="constaxonomy_out" label="${tool.name} on ${on_string}: pick.cons.taxonomy"> <filter>constaxonomy_in != None</filter> </data> <!-- format should be set to match input --> <data format_source="otucorr_in" name="otucorr_out" label="${tool.name} on ${on_string}: pick.otu.corr"> <filter>otucorr_in != None</filter> </data> <data format_source="constaxonomy_in" name="constaxonomy_out" label="${tool.name} on ${on_string}: pick.cons.taxonomy"> <filter>constaxonomy_in != None</filter> </data> </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 remove.otulabels_ command removes otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected. .. _classify.otu: http://www.mothur.org/wiki/Classify.otu .. _corr.axes: http://www.mothur.org/wiki/Corr.axes .. _otu.association: http://www.mothur.org/wiki/Otu.association .. _remove.otulabels: http://www.mothur.org/wiki/Remove.otulabels </help> </tool>