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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_alpha-rarefaction" name="qiime diversity alpha-rarefaction" version="2019.4">
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3 <description> - Alpha rarefaction curves</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime diversity alpha-rarefaction
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9
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10 --i-table=$itable
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6
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11
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12
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13 #if str($pmaxdepth):
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14 --p-max-depth="$pmaxdepth"
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15 #end if
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0
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16
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17 #if str($iphylogeny) != 'None':
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18 --i-phylogeny=$iphylogeny
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19 #end if
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20
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21 #if str($pmetrics) != 'None':
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22 --p-metrics=$pmetrics
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23 #end if
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24
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25
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6
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26 #if str($pmindepth):
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0
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27 --p-min-depth=$pmindepth
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28 #end if
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29
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6
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30 #if str($psteps):
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31 --p-steps=$psteps
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32 #end if
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33
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6
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34 #if str($piterations):
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0
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35 --p-iterations=$piterations
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36 #end if
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37
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38 #if $input_files_mmetadatafile:
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39 #def list_dict_to_string(list_dict):
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40 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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41 #for d in list_dict[1:]:
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6
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42 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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43 #end for
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44 #return $file_list
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45 #end def
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46 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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47 #end if
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48
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49 --o-visualization=ovisualization
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50 ;
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51 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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52 && cp -r out/* '$ovisualization.files_path'
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53 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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54 ]]></command>
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55 <inputs>
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56 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to compute rarefaction curves from. [required]" name="itable" optional="False" type="data"/>
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57 <param label="--p-max-depth: INTEGER The maximum rarefaction depth. Must be greater than Range(1, None) min-depth. [required]" name="pmaxdepth" optional="False" min="1" value="" type="integer"/>
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58 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Optional phylogeny for phylogenetic metrics. Phylogeny[Rooted] [optional]" name="iphylogeny" optional="True" type="data"/>
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59 <param label="--p-metrics: " name="pmetrics" optional="True" type="select">
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60 <option selected="True" value="None">Selection is Optional</option>
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61 <option value="dominance">dominance</option>
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62 <option value="ace">ace</option>
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63 <option value="brillouin_d">brillouin_d</option>
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64 <option value="margalef">margalef</option>
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65 <option value="menhinick">menhinick</option>
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66 <option value="mcintosh_d">mcintosh_d</option>
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67 <option value="berger_parker_d">berger_parker_d</option>
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68 <option value="enspie">enspie</option>
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69 <option value="doubles">doubles</option>
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70 <option value="lladser_pe">lladser_pe</option>
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71 <option value="observed_otus">observed_otus</option>
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72 <option value="faith_pd">faith_pd</option>
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73 <option value="simpson_e">simpson_e</option>
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74 <option value="robbins">robbins</option>
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75 <option value="shannon">shannon</option>
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76 <option value="pielou_e">pielou_e</option>
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77 <option value="singles">singles</option>
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78 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
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79 <option value="heip_e">heip_e</option>
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80 <option value="mcintosh_e">mcintosh_e</option>
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81 <option value="fisher_alpha">fisher_alpha</option>
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82 <option value="goods_coverage">goods_coverage</option>
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83 <option value="chao1">chao1</option>
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84 <option value="gini_index">gini_index</option>
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85 <option value="simpson">simpson</option>
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86 </param>
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87 <param label="--p-min-depth: INTEGER The minimum rarefaction depth. Range(1, None) [default: 1]" name="pmindepth" optional="True" type="integer" min="1" value="1"/>
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88 <param label="--p-steps: INTEGER The number of rarefaction depths to include between Range(2, None) min-depth and max-depth. [default: 10]" name="psteps" optional="True" type="integer" min="2" value="10"/>
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89 <param label="--p-iterations: INTEGER The number of rarefied feature tables to compute at Range(1, None) each step. [default: 10]" name="piterations" optional="True" type="integer" min="1" value="10"/>
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90
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91 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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92 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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93 </repeat>
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94
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95 </inputs>
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96 <outputs>
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97 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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98 </outputs>
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99 <help><![CDATA[
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100 Alpha rarefaction curves
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101 ########################
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102
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103 Generate interactive alpha rarefaction curves by computing rarefactions
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104 between `min_depth` and `max_depth`. The number of intermediate depths to
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105 compute is controlled by the `steps` parameter, with n `iterations` being
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106 computed at each rarefaction depth. If sample metadata is provided, samples
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107 may be grouped based on distinct values within a metadata column.
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108
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109 Parameters
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110 ----------
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111 table : FeatureTable[Frequency]
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112 Feature table to compute rarefaction curves from.
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113 max_depth : Int % Range(1, None)
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114 The maximum rarefaction depth. Must be greater than min_depth.
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115 phylogeny : Phylogeny[Rooted], optional
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116 Optional phylogeny for phylogenetic metrics.
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117 metrics : Set[Str % Choices('pielou_e', 'simpson_e', 'shannon', 'margalef', 'menhinick', 'brillouin_d', 'mcintosh_e', 'doubles', 'robbins', 'simpson', 'enspie', 'fisher_alpha', 'heip_e', 'singles', 'michaelis_menten_fit', 'observed_otus', 'gini_index', 'dominance', 'goods_coverage', 'mcintosh_d', 'faith_pd', 'ace', 'chao1', 'lladser_pe', 'berger_parker_d')], optional
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118 The metrics to be measured. By default computes observed_otus, shannon,
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119 and if phylogeny is provided, faith_pd.
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120 metadata : Metadata, optional
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121 The sample metadata.
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122 min_depth : Int % Range(1, None), optional
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123 The minimum rarefaction depth.
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124 steps : Int % Range(2, None), optional
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125 The number of rarefaction depths to include between min_depth and
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126 max_depth.
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127 iterations : Int % Range(1, None), optional
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128 The number of rarefied feature tables to compute at each step.
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129
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130 Returns
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131 -------
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132 visualization : Visualization
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133 ]]></help>
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134 <macros>
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135 <import>qiime_citation.xml</import>
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136 </macros>
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137 <expand macro="qiime_citation"/>
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138 </tool>
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