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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility"
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3 version="2020.8">
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4 <description>Generate interactive volatility plot</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime longitudinal volatility
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10
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11 #if str($itable) != 'None':
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12 --i-table=$itable
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13 #end if
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14 # if $input_files_mmetadatafile:
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15 # def list_dict_to_string(list_dict):
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16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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17 # for d in list_dict[1:]:
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18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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19 # end for
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20 # return $file_list
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21 # end def
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22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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23 # end if
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24
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25 #if '__ob__' in str($pstatecolumn):
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26 #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
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27 #set $pstatecolumn = $pstatecolumn_temp
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28 #end if
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29 #if '__cb__' in str($pstatecolumn):
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30 #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
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31 #set $pstatecolumn = $pstatecolumn_temp
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32 #end if
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33 #if 'X' in str($pstatecolumn):
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34 #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
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35 #set $pstatecolumn = $pstatecolumn_temp
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36 #end if
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37 #if '__sq__' in str($pstatecolumn):
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38 #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
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39 #set $pstatecolumn = $pstatecolumn_temp
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40 #end if
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41 #if '__db__' in str($pstatecolumn):
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42 #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
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43 #set $pstatecolumn = $pstatecolumn_temp
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44 #end if
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45
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46 --p-state-column=$pstatecolumn
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47
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48
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49 #if '__ob__' in str($pindividualidcolumn):
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50 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
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51 #set $pindividualidcolumn = $pindividualidcolumn_temp
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52 #end if
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53 #if '__cb__' in str($pindividualidcolumn):
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54 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
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55 #set $pindividualidcolumn = $pindividualidcolumn_temp
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56 #end if
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57 #if 'X' in str($pindividualidcolumn):
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58 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
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59 #set $pindividualidcolumn = $pindividualidcolumn_temp
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60 #end if
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61 #if '__sq__' in str($pindividualidcolumn):
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62 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
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63 #set $pindividualidcolumn = $pindividualidcolumn_temp
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64 #end if
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65 #if '__db__' in str($pindividualidcolumn):
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66 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
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67 #set $pindividualidcolumn = $pindividualidcolumn_temp
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68 #end if
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69
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70 #if str($pindividualidcolumn):
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71 --p-individual-id-column=$pindividualidcolumn
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72 #end if
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73
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74 #if '__ob__' in str($pdefaultgroupcolumn):
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75 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__ob__', '[')
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76 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
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77 #end if
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78 #if '__cb__' in str($pdefaultgroupcolumn):
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79 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__cb__', ']')
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80 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
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81 #end if
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82 #if 'X' in str($pdefaultgroupcolumn):
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83 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('X', '\\')
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84 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
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85 #end if
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86 #if '__sq__' in str($pdefaultgroupcolumn):
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87 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__sq__', "'")
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88 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
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89 #end if
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90 #if '__db__' in str($pdefaultgroupcolumn):
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91 #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__db__', '"')
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92 #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
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93 #end if
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94
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95 #if str($pdefaultgroupcolumn):
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96 --p-default-group-column=$pdefaultgroupcolumn
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97 #end if
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98
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99 #if str($pdefaultmetric):
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100 --p-default-metric=$pdefaultmetric
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101 #end if
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102 #if str($pyscale) != 'None':
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103 --p-yscale=$pyscale
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104 #end if
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105
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106 --o-visualization=ovisualization
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107
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108 #if str($examples) != 'None':
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109 --examples=$examples
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110 #end if
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111
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112 ;
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113 cp odistancematrix.qza $odistancematrix
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114
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115 ;
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116 qiime tools export ovisualization.qzv --output-path out
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117 && mkdir -p '$ovisualization.files_path'
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118 && cp -r out/* '$ovisualization.files_path'
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119 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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120
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121 ;
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122 qiime tools export ovisualization.qzv --output-path out
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123 && mkdir -p '$ovisualization.files_path'
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124 && cp -r out/* '$ovisualization.files_path'
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125 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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126
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127 ;
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128 qiime tools export ovisualization.qzv --output-path out
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129 && mkdir -p '$ovisualization.files_path'
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130 && cp -r out/* '$ovisualization.files_path'
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131 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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132
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133 ;
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134 qiime tools export ovisualization.qzv --output-path out
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135 && mkdir -p '$ovisualization.files_path'
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136 && cp -r out/* '$ovisualization.files_path'
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137 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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138
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139 ]]></command>
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140 <inputs>
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141 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metrics. [optional]" name="itable" optional="False" type="data" />
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142 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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143 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata file containing arguments will be individual-id-column. merged) [required]" name="additional_input" optional="False" type="data" />
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144 </repeat>
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145 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
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146 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [optional]" name="pindividualidcolumn" optional="False" type="text" />
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147 <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="False" type="text" />
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148 <param label="--p-default-metric: TEXT Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization). [optional]" name="pdefaultmetric" optional="False" type="text" />
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149 <param label="--p-yscale: " name="pyscale" optional="True" type="select">
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150 <option selected="True" value="None">Selection is Optional</option>
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151 <option value="linear">linear</option>
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152 <option value="pow">pow</option>
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153 <option value="sqrt">sqrt</option>
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154 <option value="log">log</option>
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155 </param>
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156 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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157
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158 </inputs>
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159
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160 <outputs>
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161 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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162
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163 </outputs>
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164
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165 <help><![CDATA[
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166 Generate interactive volatility plot
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167 ###############################################################
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168
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169 Generate an interactive control chart depicting the longitudinal volatility
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170 of sample metadata and/or feature frequencies across time (as set using the
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171 "state_column" parameter). Any numeric metadata column (and metadata-
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172 transformable artifacts, e.g., alpha diversity results) can be plotted on
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173 the y-axis, and are selectable using the "metric_column" selector. Metric
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174 values are averaged to compare across any categorical metadata column using
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175 the "group_column" selector. Longitudinal volatility for individual
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176 subjects sampled over time is co-plotted as "spaghetti" plots if the
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177 "individual_id_column" parameter is used. state_column will typically be a
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178 measure of time, but any numeric metadata column can be used.
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179
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180 Parameters
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181 ----------
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182 metadata : Metadata
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183 Sample metadata file containing individual_id_column.
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184 state_column : Str
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185 Metadata column containing state (time) variable information.
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186 individual_id_column : Str, optional
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187 Metadata column containing IDs for individual subjects.
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188 default_group_column : Str, optional
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189 The default metadata column on which to separate groups for comparison
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190 (all categorical metadata columns will be available in the
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191 visualization).
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192 default_metric : Str, optional
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193 Numeric metadata or artifact column to test by default (all numeric
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194 metadata columns will be available in the visualization).
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195 table : FeatureTable[RelativeFrequency], optional
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196 Feature table containing metrics.
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197 yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional
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198 y-axis scaling strategy to apply.
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199
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200 Returns
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201 -------
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202 visualization : Visualization
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203 ]]></help>
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204 <macros>
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205 <import>qiime_citation.xml</import>
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206 </macros>
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207 <expand macro="qiime_citation"/>
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208 </tool> |
