Mercurial > repos > jjohnson > mothur_toolsuite
annotate 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 |
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children | 95d75b35e4d2 |
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Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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1 <tool id="mothur_get_otulabels" name="Get.otulabels" version="1.26.0"> |
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2 <description>Selects OTU labels</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 #import re, os.path |
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6 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
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7 ## adds .pick before the last extension to the input file |
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8 --cmd='get.otulabels' |
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9 --outputdir='$logfile.extra_files_path' |
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10 --accnos=$accnos |
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11 #if $constaxonomy_in.__str__ != "None" and len($constaxonomy_in.__str__) > 0: |
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12 --constaxonomy=$constaxonomy_in |
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13 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($constaxonomy_in.__str__)) + ":'" + $constaxonomy_out.__str__] |
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14 #end if |
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15 #if $otucorr_in.__str__ != "None" and len($otucorr_in.__str__) > 0: |
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16 --otucorr=$otucorr_in |
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17 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($otucorr_in.__str__)) + ":'" + $otucorr_out.__str__] |
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18 #end if |
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19 #if $corraxes_in.__str__ != "None" and len($corraxes_in.__str__) > 0: |
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20 --corraxes=$corraxes_in |
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21 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($corraxes_in.__str__)) + ":'" + $corraxes_out.__str__] |
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22 #end if |
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23 --result=#echo ','.join($results) |
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24 </command> |
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25 <inputs> |
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26 <param name="accnos" type="data" format="otulabels" label="accnos - otulabels" help="At least one of constaxonomy, otucorr, or corraxes must be given"/> |
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27 <param name="constaxonomy_in" type="data" format="cons.taxonomy" optional="true" label="constaxonomy - Consensus Taxonomy from classify.otu"/> |
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28 <param name="otucorr_in" type="data" format="otu.corr" optional="true" label="otucorr - OTU correlation from otu.association"/> |
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29 <param name="corraxes_in" type="data" format="axes" optional="true" label="corraxes - axes from corr.axes"/> |
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30 </inputs> |
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31 <outputs> |
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32 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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33 <!-- format should be set to match input --> |
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34 <data format_source="constaxonomy_in" name="constaxonomy_out" label="${tool.name} on ${on_string}: pick.cons.taxonomy"> |
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35 <filter>constaxonomy_in != None</filter> |
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36 </data> |
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37 <!-- format should be set to match input --> |
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38 <data format_source="otucorr_in" name="otucorr_out" label="${tool.name} on ${on_string}: pick.otu.corr"> |
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39 <filter>otucorr_in != None</filter> |
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40 </data> |
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41 <data format_source="constaxonomy_in" name="constaxonomy_out" label="${tool.name} on ${on_string}: pick.cons.taxonomy"> |
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42 <filter>constaxonomy_in != None</filter> |
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43 </data> |
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44 </outputs> |
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45 <requirements> |
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46 <requirement type="package" version="1.27">mothur</requirement> |
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47 </requirements> |
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48 <tests> |
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49 </tests> |
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50 <help> |
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51 **Mothur Overview** |
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52 |
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53 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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54 in the Department of Microbiology and Immunology at The University of Michigan, |
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55 provides bioinformatics for the microbial ecology community. |
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56 |
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57 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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58 |
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59 **Command Documenation** |
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60 |
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61 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. |
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62 |
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63 .. _classify.otu: http://www.mothur.org/wiki/Classify.otu |
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64 .. _corr.axes: http://www.mothur.org/wiki/Corr.axes |
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65 .. _otu.association: http://www.mothur.org/wiki/Otu.association |
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66 .. _get.otulabels: http://www.mothur.org/wiki/Get.otulabels |
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67 |
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68 </help> |
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69 </tool> |