Mercurial > repos > iuc > mothur_otu_association

annotate otu.association.xml @ 4:12af8c375bb8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author iuc
date Mon, 23 Apr 2018 10:02:44 -0400
parents 3c42f300324e
children 7cfe3ddd183a
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1 <tool profile="16.07" id="mothur_otu_association" name="Otu.association" version="@WRAPPER_VERSION@.0">
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2 <description>Calculate the correlation coefficient for the otus</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$otu' otu.dat &&
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14 ln -s '$metadata' metadata.dat &&
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15
2
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16 echo 'otu.association(
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17 #if $otu.is_of_type("mothur.relabund"):
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18 relabund=otu.dat
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19 #elif $otu.is_of_type("mothur.shared"):
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20 shared=otu.dat
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21 #end if
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22 #if $label:
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23 ,label=${ str($label).replace(",","-") }
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24 #end if
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25 #if $groups:
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26 ,groups=${ str($groups).replace(",","-") }
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27 #end if
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28 #if $method:
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29 ,method=$method
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30 #end if
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31 #if $metadata:
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32 ,metadata=metadata.dat
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33 #end if
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34 #if $cutoff:
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35 ,cutoff=$cutoff
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36 #end if
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37 )'
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38 | sed 's/ //g' ## mothur trips over whitespace
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39 | mothur
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40 | tee mothur.out.log
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41 ]]></command>
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42 <inputs>
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43 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
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44 <param name="label" type="select" label="label - OTU Labels" multiple="true" help="By default all labels are used">
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45 <expand macro="labeloptions"/>
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46 </param>
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47 <param name="groups" type="select" label="groups - Groups to include" multiple="true">
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48 <options>
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49 <filter type="data_meta" ref="otu" key="groups"/>
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50 </options>
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51 </param>
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52 <param name="method" type="select" label="method - Normalization method">
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53 <option value="pearson" selected="true">pearson</option>
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54 <option value="spearman">spearman</option>
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55 <option value="kendall">kendall</option>
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56 </param>
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57 <param name="metadata" type="data" format="tabular" optional="true" label="metadata - find the association between the otus and the metadata."/>
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58 <param name="cutoff" type="float" value="" min="0" max="1" optional="true" label="cutoff - set a pvalue at which the otu will be reported"/>
2
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59 <expand macro="param-savelog"/>
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60 </inputs>
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61 <outputs>
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62 <expand macro="logfile-output"/>
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63 <collection name="correlations" type="list" label="${tool.name} on ${on_string}: correlation coefficient files per OTU label">
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64 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otu\.corr" format="mothur.otu.corr"/>
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65 </collection>
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66 </outputs>
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67 <tests>
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68 <test><!-- test with shared file and default settings -->
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69 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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70 <output_collection name="correlations" count="36">
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71 <element name="0.41.pearson" md5="ba93b529a7b0e5ca3baa8fe9a41b4107" ftype="mothur.otu.corr"/>
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72 </output_collection>
2
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73 <param name="savelog" value="true"/>
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74 <expand macro="logfile-test"/>
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75 </test>
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76 <test><!-- test with relabund file and label and group select -->
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77 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
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78 <param name="method" value="kendall"/>
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79 <param name="label" value="0.03,0.05,0.36,0.41,0.55"/>
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80 <param name="groups" value="forest,pasture"/>
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81 <output_collection name="correlations" count="5">
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82 <element name="0.41.kendall" md5="f01da5dc45d0bae35b692a7306bdc581" ftype="mothur.otu.corr"/>
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83 </output_collection>
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84 <param name="savelog" value="true"/>
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85 <expand macro="logfile-test"/>
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86 </test>
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87 </tests>
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88 <help><![CDATA[
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89
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90 @MOTHUR_OVERVIEW@
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91
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92 **Command Documentation**
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93
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94 The otu.association_ command calculates the correlation coefficient for the otus in a shared_ or relabund_ file.
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95
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96 .. _shared: https://www.mothur.org/wiki/Shared_file
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97 .. _relabund: https://www.mothur.org/wiki/Get.relabund
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98 .. _otu.association: https://www.mothur.org/wiki/Otu.association
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99
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100 v.1.25.0: Updated to mothur 1.33, added cutoff option
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101
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102 ]]></help>
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103 <expand macro="citations"/>
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104 </tool>