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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_core-metrics" name="qiime diversity core-metrics" version="2018.4">
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3 <description> - Core diversity metrics (non-phylogenetic)</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 core-metrics --i-table=$itable
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9
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10 #def list_dict_to_string(list_dict):
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11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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12 #for d in list_dict[1:]:
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13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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14 #end for
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15 #return $file_list
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16 #end def
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17
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18 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-sampling-depth="$psamplingdepth"
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19
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20 #if str($cmdconfig) != 'None':
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21 --cmd-config=$cmdconfig
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22 #end if
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23
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24 --o-jaccard-pcoa-results=ojaccardpcoaresults --o-jaccard-emperor=ojaccardemperor --o-shannon-vector=oshannonvector --o-bray-curtis-distance-matrix=obraycurtisdistancematrix --o-bray-curtis-emperor=obraycurtisemperor --o-rarefied-table=orarefiedtable --o-jaccard-distance-matrix=ojaccarddistancematrix
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25
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26 #set $pnjobs = '${GALAXY_SLOTS:-4}'
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27
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28 #if str($pnjobs):
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29 --p-n-jobs="$pnjobs"
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30 #end if
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31
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32 --o-evenness-vector=oevennessvector --o-bray-curtis-pcoa-results=obraycurtispcoaresults --o-observed-otus-vector=oobservedotusvector;
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33
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34 cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
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35
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36 qiime tools export ojaccardemperor.qzv --output-dir out && mkdir -p '$ojaccardemperor.files_path'
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37 && cp -r out/* '$ojaccardemperor.files_path'
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38 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor';
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39
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40 cp oshannonvector.qza $oshannonvector;
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41 cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
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42
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43 qiime tools export obraycurtisemperor.qzv --output-dir out && mkdir -p '$obraycurtisemperor.files_path'
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44 && cp -r out/* '$obraycurtisemperor.files_path'
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45 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';
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46
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47 cp orarefiedtable.qza $orarefiedtable;
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48 cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
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49 cp oevennessvector.qza $oevennessvector;
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50 cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
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51 cp oobservedotusvector.qza $oobservedotusvector;
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52 ]]></command>
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53 <inputs>
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54 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data"/>
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55 <param label="--p-sampling-depth: The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" type="text"/>
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56 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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57 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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58 </repeat>
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59 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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60 </inputs>
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61 <outputs>
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62 <data format="qza" label="${tool.name} on ${on_string}: rarefied-table.qza" name="orarefiedtable"/>
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63 <data format="qza" label="${tool.name} on ${on_string}: observed-otus-vector.qza" name="oobservedotusvector"/>
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64 <data format="qza" label="${tool.name} on ${on_string}: shannon-vector.qza" name="oshannonvector"/>
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65 <data format="qza" label="${tool.name} on ${on_string}: evenness-vector.qza" name="oevennessvector"/>
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66 <data format="qza" label="${tool.name} on ${on_string}: jaccard-distance-matrix.qza" name="ojaccarddistancematrix"/>
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67 <data format="qza" label="${tool.name} on ${on_string}: bray-curtis-distance-matrix.qza" name="obraycurtisdistancematrix"/>
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68 <data format="qza" label="${tool.name} on ${on_string}: jaccard-pcoa-results.qza" name="ojaccardpcoaresults"/>
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69 <data format="qza" label="${tool.name} on ${on_string}: bray-curtis-pcoa-results.qza" name="obraycurtispcoaresults"/>
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70 <data format="html" label="${tool.name} on ${on_string}: jaccard-emperor.qzv" name="ojaccardemperor"/>
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71 <data format="html" label="${tool.name} on ${on_string}: bray-curtis-emperor.qzv" name="obraycurtisemperor"/>
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72 </outputs>
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73 <help><![CDATA[
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74 Core diversity metrics (non-phylogenetic)
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75 -----------------------------------------
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76
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77 Applies a collection of diversity metrics (non-phylogenetic) to a feature
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78 table.
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79
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80 Parameters
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81 ----------
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82 table : FeatureTable[Frequency]
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83 The feature table containing the samples over which diversity metrics
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84 should be computed.
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85 sampling_depth : Int % Range(1, None)
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86 The total frequency that each sample should be rarefied to prior to
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87 computing diversity metrics.
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88 metadata : Metadata
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89 The sample metadata to use in the emperor plots.
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90
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91 Returns
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92 -------
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93 rarefied_table : FeatureTable[Frequency]
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94 The resulting rarefied feature table.
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95 observed_otus_vector : SampleData[AlphaDiversity]
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96 Vector of Observed OTUs values by sample.
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97 shannon_vector : SampleData[AlphaDiversity]
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98 Vector of Shannon diversity values by sample.
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99 evenness_vector : SampleData[AlphaDiversity]
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100 Vector of Pielou's evenness values by sample.
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101 jaccard_distance_matrix : DistanceMatrix
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102 Matrix of Jaccard distances between pairs of samples.
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103 bray_curtis_distance_matrix : DistanceMatrix
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104 Matrix of Bray-Curtis distances between pairs of samples.
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105 jaccard_pcoa_results : PCoAResults
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106 PCoA matrix computed from Jaccard distances between samples.
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107 bray_curtis_pcoa_results : PCoAResults
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108 PCoA matrix computed from Bray-Curtis distances between samples.
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109 jaccard_emperor : Visualization
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110 Emperor plot of the PCoA matrix computed from Jaccard.
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111 bray_curtis_emperor : Visualization
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112 Emperor plot of the PCoA matrix computed from Bray-Curtis.
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113 ]]>
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114 </help>
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115 </tool>
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