Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/get.otulabels.xml @ 27:49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 04 Dec 2012 11:05:19 -0600 |
parents | |
children | 95d75b35e4d2 |
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<tool id="mothur_get_otulabels" name="Get.otulabels" version="1.26.0"> <description>Selects OTU labels</description> <command interpreter="python"> mothur_wrapper.py #import re, os.path #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] ## adds .pick before the last extension to the input file --cmd='get.otulabels' --outputdir='$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" help="At least one of constaxonomy, otucorr, or corraxes must be given"/> <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 get.otulabels_ command selects 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 .. _get.otulabels: http://www.mothur.org/wiki/Get.otulabels </help> </tool>