Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/corr.axes.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
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7 | 1 <tool id="mothur_corr_axes" name="Corr.axes" version="1.20.0"> |
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2 <description>correlation of data to axes</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 ## output {group_file_name}.pick.{label}.groups {list_file_name}.pick.{label}.list |
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6 #import re, os.path |
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7 --cmd='corr.axes' |
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8 --outputdir='$logfile.extra_files_path' |
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9 #if $input.source == 'shared': |
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10 #if isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): |
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11 --shared=$input.otu |
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12 #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__): |
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13 --relabund=$input.otu |
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14 #end if |
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15 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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16 --label=$input.label |
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17 #end if |
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18 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: |
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19 --groups=$input.groups |
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20 #end if |
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21 #else: |
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22 --metadata=$input.metadata |
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23 #end if |
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24 --method=$method |
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25 --axes=$axes |
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26 #if int($numaxes.__str__) > 0: |
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27 --numaxes=$numaxes |
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28 #end if |
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29 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.corr.axes$:'$corr_axes |
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30 </command> |
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31 <inputs> |
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32 <param name="axes" type="data" format="axes" label="axes - a pcoa axes dataset"/> |
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33 <conditional name="input"> |
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34 <param name="source" type="select" label="Generate Collector Curvers for"> |
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35 <option value="shared">OTU Shared or Relabund</option> |
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36 <option value="metadata">Metadata table</option> |
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37 </param> |
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38 <when value="shared"> |
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39 <param name="otu" type="data" format="shared,relabund" label="shared or relabund - OTU Shared or Relabund"/> |
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40 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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41 <options> |
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42 <filter type="data_meta" ref="otu" key="labels" /> |
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43 </options> |
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44 </param> |
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45 <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true"> |
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46 <options> |
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47 <filter type="data_meta" ref="otu" key="groups" /> |
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48 </options> |
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49 </param> |
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50 </when> |
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51 <when value="metadata"> |
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52 <param name="metadata" type="data" format="tabular" label="metadata - Table of floating point values" |
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53 help="metadata has the same number of rows as the samples, but the column(s) are floats that describe the samples (e.g. temperature, weight, etc.)"/> |
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54 </when> |
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55 </conditional> |
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56 <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson" > |
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57 <option value="pearson" selected="true">pearson</option> |
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58 <option value="spearman">spearman</option> |
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59 <option value="kendall">kendall</option> |
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60 </param> |
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61 <param name="numaxes" type="integer" value="3" label="numaxes - Number of axes to use (default 3)"/> |
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62 </inputs> |
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63 <outputs> |
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64 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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65 <data format="axes" name="corr_axes" label="${tool.name} on ${on_string}: corr.axes"/> |
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66 </outputs> |
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67 <requirements> |
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68 <requirement type="package" version="1.27">mothur</requirement> |
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69 </requirements> |
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70 <tests> |
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71 </tests> |
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72 <help> |
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73 **Mothur Overview** |
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74 |
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75 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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76 in the Department of Microbiology and Immunology at The University of Michigan, |
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77 provides bioinformatics for the microbial ecology community. |
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78 |
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79 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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80 |
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81 **Command Documenation** |
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82 |
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83 The corr.axes_ command calculates the correlation of data to axes. |
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84 |
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85 .. _corr.axes: http://www.mothur.org/wiki/Corr.axes |
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86 |
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87 |
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88 </help> |
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89 </tool> |