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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="2018.4">
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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="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime diversity alpha-rarefaction --p-max-depth="$pmaxdepth" --i-table=$itable
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9
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10 #if str($pmetrics) != 'None':
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11 --p-metrics=$pmetrics
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12 #end if
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13
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14 #if $pmindepth:
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15 --p-min-depth=$pmindepth
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16 #end if
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17
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18 #if $piterations:
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19 --p-iterations=$piterations
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20 #end if
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21
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22 #if str($cmdconfig) != 'None':
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23 --cmd-config=$cmdconfig
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24 #end if
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25
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26 #if $input_files_mmetadatafile:
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27
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28 #def list_dict_to_string(list_dict):
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29 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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30 #for d in list_dict[1:]:
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31 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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32 #end for
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33 #return $file_list
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34 #end def
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35 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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36 #end if
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37
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38 #if $psteps:
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39 --p-steps=$psteps
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40 #end if
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41
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42 #if str($iphylogeny) != 'None':
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43 --i-phylogeny=$iphylogeny
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44 #end if
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45
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46 --o-visualization=ovisualization;
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47 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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48 && cp -r out/* '$ovisualization.files_path'
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49 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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50 ]]></command>
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51 <inputs>
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52 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table to compute rarefaction curves from. [required]" name="itable" optional="False" type="data"/>
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53 <param label="--p-max-depth: The maximum rarefaction depth. Must be greater than min_depth. [required]" name="pmaxdepth" optional="False" type="text"/>
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54 <param format="qza,no_unzip.zip" label="--i-phylogeny: Phylogeny[Rooted] Optional phylogeny for phylogenetic metrics. [optional]" name="iphylogeny" optional="True" type="data"/>
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55 <param name="pmetrics" optional="True" type="select" label="--p-metrics: The metrics to be measured. By default
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56 computes observed_otus, shannon, and if
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57 phylogeny is provided, faith_pd. [optional]">
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58 <option selected="True" value="None">Selection is Optional</option>
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59 <option value="goods_coverage">goods_coverage</option>
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60 <option value="heip_e">heip_e</option>
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61 <option value="mcintosh_d">mcintosh_d</option>
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62 <option value="observed_otus">observed_otus</option>
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63 <option value="doubles">doubles</option>
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64 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
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65 <option value="shannon">shannon</option>
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66 <option value="margalef">margalef</option>
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67 <option value="simpson">simpson</option>
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68 <option value="lladser_pe">lladser_pe</option>
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69 <option value="menhinick">menhinick</option>
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70 <option value="singles">singles</option>
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71 <option value="gini_index">gini_index</option>
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72 <option value="robbins">robbins</option>
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73 <option value="ace">ace</option>
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74 <option value="simpson_e">simpson_e</option>
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75 <option value="enspie">enspie</option>
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76 <option value="berger_parker_d">berger_parker_d</option>
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77 <option value="fisher_alpha">fisher_alpha</option>
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78 <option value="dominance">dominance</option>
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79 <option value="pielou_e">pielou_e</option>
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80 <option value="chao1">chao1</option>
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81 <option value="mcintosh_e">mcintosh_e</option>
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82 <option value="faith_pd">faith_pd</option>
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83 <option value="brillouin_d">brillouin_d</option>
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84 </param>
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85 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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86 <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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87 </repeat>
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88 <param label="--p-min-depth: The minimum rarefaction depth. [default: 1]" name="pmindepth" optional="True" type="integer" value="1"/>
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89 <param label="--p-steps: The number of rarefaction depths to include between min_depth and max_depth. [default: 10]" name="psteps" optional="True" type="integer" value="10"/>
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90 <param label="--p-iterations: The number of rarefied feature tables to compute at each step. [default: 10]" name="piterations" optional="True" type="integer" value="10"/>
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91 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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92 </inputs>
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93 <outputs>
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94 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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95 </outputs>
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96 <help><![CDATA[
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97 Alpha rarefaction curves
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98 -------------------------
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99
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100 Generate interactive alpha rarefaction curves by computing rarefactions
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101 between \`min_depth\` and \`max_depth\`. The number of intermediate depths to
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102 compute is controlled by the \`steps\` parameter, with n \`iterations\` being
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103 computed at each rarefaction depth. If sample metadata is provided, samples
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104 may be grouped based on distinct values within a metadata column.
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105
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106 Parameters
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107 ----------
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108 table : FeatureTable[Frequency]
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109 Feature table to compute rarefaction curves from.
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110 phylogeny : Phylogeny[Rooted], optional
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111 Optional phylogeny for phylogenetic metrics.
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112 max_depth : Int % Range(1, None)
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113 The maximum rarefaction depth. Must be greater than min_depth.
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114 metrics : Set[Str % Choices({'ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'dominance', 'doubles', 'enspie', 'faith_pd', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'observed_otus', 'pielou_e', 'robbins', 'shannon', 'simpson', 'simpson_e', 'singles'})], optional
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115 The metrics to be measured. By default computes observed_otus, shannon,
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116 and if phylogeny is provided, faith_pd.
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117 metadata : Metadata, optional
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118 The sample metadata.
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119 min_depth : Int % Range(1, None), optional
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120 The minimum rarefaction depth.
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121 steps : Int % Range(2, None), optional
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122 The number of rarefaction depths to include between min_depth and
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123 max_depth.
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124 iterations : Int % Range(1, None), optional
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125 The number of rarefied feature tables to compute at each step.
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126
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127 Returns
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128 -------
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129 visualization : Visualization
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130 \
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131 ]]>
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132 </help>
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133 <macros>
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134 <import>qiime_citation.xml</import>
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135 </macros>
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136 <expand macro="qiime_citation" />
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137 </tool>
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