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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_core-metrics-phylogenetic" name="qiime diversity core-metrics-phylogenetic" version="2019.4">
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3 <description> - Core diversity metrics (phylogenetic and non- phylogenetic)</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 core-metrics-phylogenetic
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9
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10 --i-table=$itable
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11 --i-phylogeny=$iphylogeny
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12 --p-sampling-depth="$psamplingdepth"
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13
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14 #set $pnjobs = '${GALAXY_SLOTS:-4}'
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15 #if str($pnjobs):
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16 --p-n-jobs="$pnjobs"
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17 #end if
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18
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19 #def list_dict_to_string(list_dict):
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20 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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21 #for d in list_dict[1:]:
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22 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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23 #end for
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24 #return $file_list
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25 #end def
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26
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27 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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28
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29
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30 --o-rarefied-table=orarefiedtable
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31 --o-faith-pd-vector=ofaithpdvector
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32 --o-observed-otus-vector=oobservedotusvector
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33 --o-shannon-vector=oshannonvector
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34 --o-evenness-vector=oevennessvector
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35 --o-unweighted-unifrac-distance-matrix=ounweightedunifracdistancematrix
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36 --o-weighted-unifrac-distance-matrix=oweightedunifracdistancematrix
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37 --o-jaccard-distance-matrix=ojaccarddistancematrix
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38 --o-bray-curtis-distance-matrix=obraycurtisdistancematrix
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39 --o-unweighted-unifrac-pcoa-results=ounweightedunifracpcoaresults
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40 --o-weighted-unifrac-pcoa-results=oweightedunifracpcoaresults
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41 --o-jaccard-pcoa-results=ojaccardpcoaresults
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42 --o-bray-curtis-pcoa-results=obraycurtispcoaresults
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43 --o-unweighted-unifrac-emperor=ounweightedunifracemperor
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44 --o-weighted-unifrac-emperor=oweightedunifracemperor
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45 --o-jaccard-emperor=ojaccardemperor
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46 --o-bray-curtis-emperor=obraycurtisemperor
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47 ;
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48 cp orarefiedtable.qza $orarefiedtable;
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49 cp ofaithpdvector.qza $ofaithpdvector;
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50 cp oobservedotusvector.qza $oobservedotusvector;
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51 cp oshannonvector.qza $oshannonvector;
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52 cp oevennessvector.qza $oevennessvector;
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53 cp ounweightedunifracdistancematrix.qza $ounweightedunifracdistancematrix;
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54 cp oweightedunifracdistancematrix.qza $oweightedunifracdistancematrix;
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55 cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
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56 cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
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57 cp ounweightedunifracpcoaresults.qza $ounweightedunifracpcoaresults;
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58 cp oweightedunifracpcoaresults.qza $oweightedunifracpcoaresults;
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59 cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
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60 cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
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61 qiime tools export --input-path ounweightedunifracemperor.qzv --output-path out && mkdir -p '$ounweightedunifracemperor.files_path'
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62 && cp -r out/* '$ounweightedunifracemperor.files_path'
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63 && mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor';
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64 qiime tools export --input-path oweightedunifracemperor.qzv --output-path out && mkdir -p '$oweightedunifracemperor.files_path'
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65 && cp -r out/* '$oweightedunifracemperor.files_path'
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66 && mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor';
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67 qiime tools export --input-path ojaccardemperor.qzv --output-path out && mkdir -p '$ojaccardemperor.files_path'
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68 && cp -r out/* '$ojaccardemperor.files_path'
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69 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor';
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70 qiime tools export --input-path obraycurtisemperor.qzv --output-path out && mkdir -p '$obraycurtisemperor.files_path'
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71 && cp -r out/* '$obraycurtisemperor.files_path'
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72 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';
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73 ]]></command>
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74 <inputs>
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75 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data"/>
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76 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data"/>
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77 <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" min="1" value="" type="integer"/>
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78
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79 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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80 <param label="--m-metadata-file: (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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81 </repeat>
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82
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83 </inputs>
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84 <outputs>
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85 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable"/>
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86 <data format="qza" label="${tool.name} on ${on_string}: faithpdvector.qza" name="ofaithpdvector"/>
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87 <data format="qza" label="${tool.name} on ${on_string}: observedotusvector.qza" name="oobservedotusvector"/>
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88 <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector"/>
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89 <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector"/>
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90 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracdistancematrix.qza" name="ounweightedunifracdistancematrix"/>
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91 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracdistancematrix.qza" name="oweightedunifracdistancematrix"/>
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92 <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix"/>
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93 <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix"/>
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94 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracpcoaresults.qza" name="ounweightedunifracpcoaresults"/>
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95 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracpcoaresults.qza" name="oweightedunifracpcoaresults"/>
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96 <data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults"/>
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97 <data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults"/>
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98 <data format="html" label="${tool.name} on ${on_string}: unweightedunifracemperor.qzv" name="ounweightedunifracemperor"/>
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99 <data format="html" label="${tool.name} on ${on_string}: weightedunifracemperor.qzv" name="oweightedunifracemperor"/>
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100 <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.qzv" name="ojaccardemperor"/>
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101 <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.qzv" name="obraycurtisemperor"/>
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102 </outputs>
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103 <help><![CDATA[
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104 Core diversity metrics (phylogenetic and non-phylogenetic)
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105 ##########################################################
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106
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107 Applies a collection of diversity metrics (both phylogenetic and non-
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108 phylogenetic) to a feature table.
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109
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110 Parameters
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111 ----------
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112 table : FeatureTable[Frequency]
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113 The feature table containing the samples over which diversity metrics
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114 should be computed.
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115 phylogeny : Phylogeny[Rooted]
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116 Phylogenetic tree containing tip identifiers that correspond to the
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117 feature identifiers in the table. This tree can contain tip ids that
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118 are not present in the table, but all feature ids in the table must be
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119 present in this tree.
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120 sampling_depth : Int % Range(1, None)
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121 The total frequency that each sample should be rarefied to prior to
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122 computing diversity metrics.
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123 metadata : Metadata
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124 The sample metadata to use in the emperor plots.
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125
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126 Returns
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127 -------
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128 rarefied_table : FeatureTable[Frequency]
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129 The resulting rarefied feature table.
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130 faith_pd_vector : SampleData[AlphaDiversity]
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131 Vector of Faith PD values by sample.
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132 observed_otus_vector : SampleData[AlphaDiversity]
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133 Vector of Observed OTUs values by sample.
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134 shannon_vector : SampleData[AlphaDiversity]
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135 Vector of Shannon diversity values by sample.
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136 evenness_vector : SampleData[AlphaDiversity]
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137 Vector of Pielou's evenness values by sample.
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138 unweighted_unifrac_distance_matrix : DistanceMatrix
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139 Matrix of unweighted UniFrac distances between pairs of samples.
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140 weighted_unifrac_distance_matrix : DistanceMatrix
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141 Matrix of weighted UniFrac distances between pairs of samples.
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142 jaccard_distance_matrix : DistanceMatrix
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143 Matrix of Jaccard distances between pairs of samples.
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144 bray_curtis_distance_matrix : DistanceMatrix
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145 Matrix of Bray-Curtis distances between pairs of samples.
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146 unweighted_unifrac_pcoa_results : PCoAResults
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147 PCoA matrix computed from unweighted UniFrac distances between samples.
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148 weighted_unifrac_pcoa_results : PCoAResults
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149 PCoA matrix computed from weighted UniFrac distances between samples.
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150 jaccard_pcoa_results : PCoAResults
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151 PCoA matrix computed from Jaccard distances between samples.
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152 bray_curtis_pcoa_results : PCoAResults
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153 PCoA matrix computed from Bray-Curtis distances between samples.
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154 unweighted_unifrac_emperor : Visualization
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155 Emperor plot of the PCoA matrix computed from unweighted UniFrac.
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156 weighted_unifrac_emperor : Visualization
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157 Emperor plot of the PCoA matrix computed from weighted UniFrac.
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158 jaccard_emperor : Visualization
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159 Emperor plot of the PCoA matrix computed from Jaccard.
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160 bray_curtis_emperor : Visualization
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161 Emperor plot of the PCoA matrix computed from Bray-Curtis.
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162 ]]></help>
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163 <macros>
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164 <import>qiime_citation.xml</import>
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165 </macros>
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166 <expand macro="qiime_citation"/>
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167 </tool>
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