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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_plot-feature-volatility" name="qiime longitudinal plot-feature-volatility"
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3 version="2020.8">
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4 <description>Plot longitudinal feature volatility and importances</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 plot-feature-volatility
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10
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11 --i-table=$itable
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12
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13 --i-importances=$iimportances
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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=$pdefaultgroupcolumn
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97 #end if
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98
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99 #if str($pyscale) != 'None':
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100 --p-yscale=$pyscale
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101 #end if
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102
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103 #if str($pimportancethreshold) != 'None':
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104 --p-importance-threshold=$pimportancethreshold
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105 #end if
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106
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107 #if str($pfeaturecount) != 'None':
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108 --p-feature-count=$pfeaturecount
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109 #end if
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110
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111 #if str($pmissingsamples) != 'None':
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112 --p-missing-samples=$pmissingsamples
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113 #end if
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114
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115 --o-visualization=ovisualization
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116
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117 #if str($examples) != 'None':
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118 --examples=$examples
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119 #end if
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120
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121 ;
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122 cp odistancematrix.qza $odistancematrix
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123
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124 ;
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125 qiime tools export ovisualization.qzv --output-path out
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126 && mkdir -p '$ovisualization.files_path'
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127 && cp -r out/* '$ovisualization.files_path'
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128 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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129
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130 ;
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131 qiime tools export ovisualization.qzv --output-path out
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132 && mkdir -p '$ovisualization.files_path'
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133 && cp -r out/* '$ovisualization.files_path'
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134 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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135
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136 ;
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137 qiime tools export ovisualization.qzv --output-path out
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138 && mkdir -p '$ovisualization.files_path'
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139 && cp -r out/* '$ovisualization.files_path'
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140 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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141
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142 ]]></command>
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143 <inputs>
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144 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing features found in importances. [required]" name="itable" optional="False" type="data" />
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145 <param format="qza,no_unzip.zip" label="--i-importances: ARTIFACT FeatureData[Importance] Feature importance scores. [required]" name="iimportances" optional="False" type="data" />
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146 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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147 <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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148 </repeat>
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149 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
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150 <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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151 <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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152 <param label="--p-yscale: " name="pyscale" optional="True" type="select">
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153 <option selected="True" value="None">Selection is Optional</option>
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154 <option value="linear">linear</option>
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155 <option value="pow">pow</option>
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156 <option value="sqrt">sqrt</option>
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157 <option value="log">log</option>
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158 </param>
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159 <param label="--p-importance-threshold: " name="pimportancethreshold" optional="True" type="select">
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160 <option selected="True" value="None">Selection is Optional</option>
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161 <option value="Float % Range(0">Float % Range(0</option>
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162 <option value="None">None</option>
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163 <option value="inclusive_start=False">inclusive_start=False</option>
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164 </param>
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165 <param label="--p-feature-count: " name="pfeaturecount" optional="True" type="select">
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166 <option selected="True" value="None">Selection is Optional</option>
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167 <option value="Int % Range(1">Int % Range(1</option>
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168 <option value="None">None</option>
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169 </param>
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170 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
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171 <option selected="True" value="None">Selection is Optional</option>
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172 <option value="error">error</option>
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173 <option value="ignore">ignore</option>
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174 </param>
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175 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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176
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177 </inputs>
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178
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179 <outputs>
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180 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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181
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182 </outputs>
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183
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184 <help><![CDATA[
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185 Plot longitudinal feature volatility and importances
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186 ###############################################################
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187
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188 Plots an interactive control chart of feature abundances (y-axis) in each
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189 sample across time (or state; x-axis). Feature importance scores and
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190 descriptive statistics for each feature are plotted in interactive bar
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191 charts below the control chart, facilitating exploration of longitudinal
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192 feature data. This visualization is intended for use with the feature-
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193 volatility pipeline; use that pipeline to access this visualization.
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194
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195 Parameters
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196 ----------
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197 table : FeatureTable[RelativeFrequency]
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198 Feature table containing features found in importances.
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199 importances : FeatureData[Importance]
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200 Feature importance scores.
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201 metadata : Metadata
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202 Sample metadata file containing individual_id_column.
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203 state_column : Str
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204 Metadata column containing state (time) variable information.
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205 individual_id_column : Str, optional
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206 Metadata column containing IDs for individual subjects.
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207 default_group_column : Str, optional
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208 The default metadata column on which to separate groups for comparison
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209 (all categorical metadata columns will be available in the
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210 visualization).
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211 yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional
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212 y-axis scaling strategy to apply.
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213 importance_threshold : Float % Range(0, None, inclusive_start=False) | Str % Choices('q1', 'q2', 'q3'), optional
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214 Filter feature table to exclude any features with an importance score
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215 less than this threshold. Set to "q1", "q2", or "q3" to select the
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216 first, second, or third quartile of values. Set to "None" to disable
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217 this filter.
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218 feature_count : Int % Range(1, None) | Str % Choices('all'), optional
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219 Filter feature table to include top N most important features. Set to
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220 "all" to include all features.
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221 missing_samples : Str % Choices('error', 'ignore'), optional
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222 How to handle missing samples in metadata. "error" will fail if missing
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223 samples are detected. "ignore" will cause the feature table and
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224 metadata to be filtered, so that only samples found in both files are
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225 retained.
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226
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227 Returns
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228 -------
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229 visualization : Visualization
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230 ]]></help>
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231 <macros>
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232 <import>qiime_citation.xml</import>
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233 </macros>
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234 <expand macro="qiime_citation"/>
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235 </tool> |
