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1 <?xml version="1.0" ?>
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2 <tool id="qiime_gneiss_balance-taxonomy" name="qiime gneiss balance-taxonomy" version="2018.4">
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3 <description>- Balance Summary</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>
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8 <![CDATA[
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9 qiime gneiss balance-taxonomy --i-tree=$itree --p-balance-name="$pbalancename"
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10
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11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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13 --i-taxonomy '$tax'
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14 #else:
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15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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16 --i-taxonomy '$tax'
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17 #end if
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18
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19 --i-table=$itable
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20 #if $pnfeatures:
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21 --p-n-features=$pnfeatures
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22 #end if
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23
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24 #if str($mmetadatacolumn):
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25 --m-metadata-column="$mmetadatacolumn"
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26 #end if
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27
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28 #if str($cmdconfig) != 'None':
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29 --cmd-config=$cmdconfig
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30 #end if
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31
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32 #if $ptaxalevel:
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33 --p-taxa-level=$ptaxalevel
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34 #end if
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35 --o-visualization=ovisualization
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36 #if $input_files_mmetadatafile:
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37
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38 #def list_dict_to_string(list_dict):
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39 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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40 #for d in list_dict[1:]:
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41 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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42 #end for
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43 #return $file_list
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44 #end def
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45 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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46 #end if
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47
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48 #if str($pthreshold):
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49 --p-threshold="$pthreshold"
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50 #end if
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51 ;
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52 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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53 && cp -r out/* '$ovisualization.files_path'
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54 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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55 ]]>
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56 </command>
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57 <inputs>
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58 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Composition] A table of compositions. [required]" name="itable" optional="False" type="data"/>
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59 <param format="qza,no_unzip.zip" label="--i-tree: Hierarchy The tree used to calculate the balances. [required]" name="itree" optional="False" type="data"/>
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60
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61 <conditional name="id_to_taxonomy_fp" optional="True">
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62 <param name="selector" type="select" label="Reference taxonomy to query">
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63 <option value="cached">Public databases</option>
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64 <option value="history">Databases from your history</option>
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65 </param>
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66 <when value="cached">
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67 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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68 <options from_data_table="qiime_taxonomy" />
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69 </param>
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70 </when>
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71 <when value="history">
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72 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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73 </when>
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74 </conditional>
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75
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76 <param label="--p-balance-name: Name of the balance to summarize. [required]" name="pbalancename" optional="False" type="text"/>
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77 <param label="--p-taxa-level: Level of taxonomy to summarize. [default: 0]" name="ptaxalevel" optional="True" type="integer" value="0"/>
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78 <param label="--p-n-features: The number of features to plot in the proportion plot. [default: 10]" name="pnfeatures" optional="True" type="integer" value="10"/>
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79 <param label="--p-threshold: A threshold to designate discrete categories for a numerical metadata column. This will split the numerical column values into two categories, values below the threshold, and values above the threshold. If not specified, this threshold will default to the mean. [optional]" name="pthreshold" optional="True" type="text"/>
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80
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81 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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82 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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83 </repeat>
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84 <param label="--m-metadata-column: MetadataColumn[Categorical | Numeric] Column from metadata file or artifact viewable as metadata. Metadata column for plotting the balance (optional). [optional]" name="mmetadatacolumn" optional="True" type="text"/>
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85
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86 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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87 </inputs>
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88 <outputs>
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89 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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90 </outputs>
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91 <help>
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92 <![CDATA[
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93 Balance Summary
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94 ----------------
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95
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96 Visualize the distribution of a single balance and summarize its numerator
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97 and denominator components.
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98
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99 Parameters
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100 ----------
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101 table : FeatureTable[Composition]
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102 A table of compositions.
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103 tree : Hierarchy
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104 The tree used to calculate the balances.
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105 taxonomy : FeatureData[Taxonomy]
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106 Taxonomy information for the OTUs.
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107 balance_name : Str
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108 Name of the balance to summarize.
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109 taxa_level : Int, optional
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110 Level of taxonomy to summarize.
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111 n_features : Int, optional
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112 The number of features to plot in the proportion plot.
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113 threshold : Float, optional
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114 A threshold to designate discrete categories for a numerical metadata
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115 column. This will split the numerical column values into two
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116 categories, values below the threshold, and values above the threshold.
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117 If not specified, this threshold will default to the mean.
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118 metadata : MetadataColumn[Categorical | Numeric], optional
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119 Metadata column for plotting the balance (optional).
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120
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121 Returns
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122 -------
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123 visualization : Visualization
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124 \
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125 ]]>
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126 </help>
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127 </tool>
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