Mercurial > repos > iuc > mothur_corr_axes

annotate corr.axes.xml @ 2:4e4035bf57df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:08:33 -0400
parents 9961b707d075
children 0968daa9b52f
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1 <tool profile="16.07" id="mothur_corr_axes" name="Corr.axes" version="@WRAPPER_VERSION@.0">
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2 <description>correlation of data to axes</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
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10 <command><![CDATA[
2
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11 @SHELL_OPTIONS@
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12
2
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13 ## create symlinks to input datasets
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14 #if $input.source == "shared":
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15 ln -s '$input.otu' input.otu.dat &&
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16 #else
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17 ln -s '$input.metadata' input.metadata.dat &&
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18 #end if
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19
2
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20 echo 'corr.axes(
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21 #if $input.source == "shared":
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22 #if $input.otu.is_of_type("mothur.relabund"):
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23 relabund=input.otu.dat,
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24 #elif $input.otu.is_of_type("mothur.shared"):
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25 shared=input.otu.dat,
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26 #end if
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27 #if $input.label:
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28 label=$input.label,
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29 #end if
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30 #if $input.groups:
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31 groups=${ str($input.groups).replace(",","-") },
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32 #end if
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33 #else:
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34 metadata=input.metadata.dat,
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35 #end if
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36 method=$method,
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37 axes=$axes,
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38 numaxes=$numaxes
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39 )'
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40 | sed 's/ //g' ## mothur trips over whitespace
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41 | mothur
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42 | tee mothur.out.log
0
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43 ]]></command>
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44 <inputs>
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45 <param name="axes" type="data" format="mothur.axes" label="axes - a pcoa axes dataset"/>
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46 <conditional name="input">
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47 <param name="source" type="select" label="Generate Collector Curvers for">
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48 <option value="shared">OTU Shared or Relabund</option>
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49 <option value="metadata">Metadata table</option>
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50 </param>
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51 <when value="shared">
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52 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/>
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53 <param name="label" type="select" label="label - OTU Labels" multiple="false" optional="true">
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54 <expand macro="labeloptions"/>
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55 </param>
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56 <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true">
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57 <options>
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58 <filter type="data_meta" ref="otu" key="groups"/>
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59 </options>
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60 </param>
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61 </when>
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62 <when value="metadata">
2
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63 <param name="metadata" type="data" format="tabular" label="metadata - Table of floating point values"
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64 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.)"/>
0
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65 </when>
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66 </conditional>
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67 <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson">
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68 <option value="pearson" selected="true">pearson</option>
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69 <option value="spearman">spearman</option>
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70 <option value="kendall">kendall</option>
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71 </param>
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72 <param name="numaxes" type="integer" value="3" min="0" label="numaxes - Number of axes to use (default 3)"/>
2
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73 <expand macro="param-savelog"/>
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74 </inputs>
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75 <outputs>
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76 <expand macro="logfile-output"/>
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77 <data name="corr_axes" format="mothur.axes" from_work_dir="input.*.axes" label="${tool.name} on ${on_string}: corr.axes"/>
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78 </outputs>
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79 <tests>
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80 <test><!-- test with shared file -->
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81 <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/>
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82 <param name="source" value="shared"/>
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83 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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84 <output name="corr_axes" md5="34ff44b9a58780bc558afd1d22d96bb1" ftype="mothur.axes"/>
2
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85 <param name="savelog" value="true"/>
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86 <expand macro="logfile-test"/>
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87 </test>
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88 <test><!-- test with metadata file -->
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89 <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/>
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90 <param name="source" value="metadata"/>
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91 <param name="metadata" value="amazon.metadata" ftype="tabular"/>
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92 <output name="corr_axes" md5="f62a3b7ed2b75312454a03ebbabe1edc" ftype="mothur.axes"/>
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93 <param name="savelog" value="true"/>
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94 <expand macro="logfile-test"/>
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95 </test>
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96 <test><!-- test with relabund file and label and group select -->
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97 <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/>
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98 <param name="source" value="shared"/>
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99 <param name="label" value="0.05"/>
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100 <param name="groups" value="forest,pasture"/>
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101 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
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102 <output name="corr_axes" md5="014f23f191ec6a9abbb82d51b3d5e24c" ftype="mothur.axes"/>
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103 <param name="savelog" value="true"/>
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104 <expand macro="logfile-test"/>
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105 </test>
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106 </tests>
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107 <help><![CDATA[
0
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108
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109 @MOTHUR_OVERVIEW@
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110
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111 **Command Documentation**
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112
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113 The corr.axes_ command calculates the correlation of data to axes.
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114
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115 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes
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116
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117 v.1.21.0: Updated to mothur 1.33
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118
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119 ]]></help>
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120 <expand macro="citations"/>
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121 </tool>