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1 <?xml version="1.0" ?>
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2 <tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences"
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3 version="2020.8">
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4 <description>Paired difference testing and boxplots</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 pairwise-differences
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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($input_files_mmetadatafile)
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23 # end if
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24
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25 --p-metric=$pmetric
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26
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27 #if '__ob__' in str($pstatecolumn):
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28 #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
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29 #set $pstatecolumn = $pstatecolumn_temp
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30 #end if
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31 #if '__cb__' in str($pstatecolumn):
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32 #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
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33 #set $pstatecolumn = $pstatecolumn_temp
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34 #end if
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35 #if 'X' in str($pstatecolumn):
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36 #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
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37 #set $pstatecolumn = $pstatecolumn_temp
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38 #end if
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39 #if '__sq__' in str($pstatecolumn):
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40 #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
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41 #set $pstatecolumn = $pstatecolumn_temp
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42 #end if
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43 #if '__db__' in str($pstatecolumn):
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44 #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
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45 #set $pstatecolumn = $pstatecolumn_temp
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46 #end if
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47
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48 --p-state-column=$pstatecolumn
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49
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50
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51 --p-state-1=$pstate1
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52
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53 --p-state-2=$pstate2
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54
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55 #if '__ob__' in str($pindividualidcolumn):
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56 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
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57 #set $pindividualidcolumn = $pindividualidcolumn_temp
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58 #end if
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59 #if '__cb__' in str($pindividualidcolumn):
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60 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
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61 #set $pindividualidcolumn = $pindividualidcolumn_temp
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62 #end if
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63 #if 'X' in str($pindividualidcolumn):
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64 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
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65 #set $pindividualidcolumn = $pindividualidcolumn_temp
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66 #end if
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67 #if '__sq__' in str($pindividualidcolumn):
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68 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
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69 #set $pindividualidcolumn = $pindividualidcolumn_temp
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70 #end if
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71 #if '__db__' in str($pindividualidcolumn):
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72 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
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73 #set $pindividualidcolumn = $pindividualidcolumn_temp
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74 #end if
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75
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76 --p-individual-id-column=$pindividualidcolumn
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77
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78
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79 #if '__ob__' in str($pgroupcolumn):
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80 #set $pgroupcolumn_temp = $pgroupcolumn.replace('__ob__', '[')
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81 #set $pgroupcolumn = $pgroupcolumn_temp
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82 #end if
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83 #if '__cb__' in str($pgroupcolumn):
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84 #set $pgroupcolumn_temp = $pgroupcolumn.replace('__cb__', ']')
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85 #set $pgroupcolumn = $pgroupcolumn_temp
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86 #end if
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87 #if 'X' in str($pgroupcolumn):
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88 #set $pgroupcolumn_temp = $pgroupcolumn.replace('X', '\\')
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89 #set $pgroupcolumn = $pgroupcolumn_temp
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90 #end if
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91 #if '__sq__' in str($pgroupcolumn):
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92 #set $pgroupcolumn_temp = $pgroupcolumn.replace('__sq__', "'")
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93 #set $pgroupcolumn = $pgroupcolumn_temp
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94 #end if
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95 #if '__db__' in str($pgroupcolumn):
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96 #set $pgroupcolumn_temp = $pgroupcolumn.replace('__db__', '"')
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97 #set $pgroupcolumn = $pgroupcolumn_temp
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98 #end if
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99
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100 #if str($pgroupcolumn):
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101 --p-group-column=$pgroupcolumn
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102 #end if
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103
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104 #if $pparametric:
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105 --p-parametric
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106 #end if
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107
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108 #if str($ppalette) != 'None':
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109 --p-palette=$ppalette
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110 #end if
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111
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112 #if str($preplicatehandling) != 'None':
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113 --p-replicate-handling=$preplicatehandling
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114 #end if
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115
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116 --o-visualization=ovisualization
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117
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118 #if str($examples) != 'None':
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119 --examples=$examples
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120 #end if
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121
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122 ;
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123 cp odistancematrix.qza $odistancematrix
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124
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125 ;
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126 qiime tools export ovisualization.qzv --output-path out
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127 && mkdir -p '$ovisualization.files_path'
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128 && cp -r out/* '$ovisualization.files_path'
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129 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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130
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131 ]]></command>
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132 <inputs>
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133 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to optionally use for paired comparisons. [optional]" name="itable" optional="False" type="data" />
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134 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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135 <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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136 </repeat>
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137 <param label="--p-metric: TEXT Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text" />
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138 <param label="--p-state-column: TEXT Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text" />
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139 <param label="--p-state-1: TEXT Baseline state column value. [required]" name="pstate1" optional="False" type="text" />
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140 <param label="--p-state-2: TEXT State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text" />
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141 <param label="--p-individual-id-column: TEXT Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state-1 or state-2, that subject will be dropped and reported in standard output by default. Set replicate_handling=\'random\' to instead randomly select one member. [required]" name="pindividualidcolumn" optional="False" type="text" />
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142 <param label="--p-group-column: TEXT Metadata column on which to separate groups for comparison [optional]" name="pgroupcolumn" optional="False" type="text" />
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143 <param label="--p-parametric: --p-parametric: / --p-no-parametric Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests. [default: False]" name="pparametric" selected="False" type="boolean" />
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144 <param label="--p-palette: " name="ppalette" optional="True" type="select">
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145 <option selected="True" value="None">Selection is Optional</option>
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146 <option value="Set1">Set1</option>
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147 <option value="Set2">Set2</option>
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148 <option value="Set3">Set3</option>
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149 <option value="Pastel1">Pastel1</option>
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150 <option value="Pastel2">Pastel2</option>
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151 <option value="Paired">Paired</option>
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152 <option value="Accent">Accent</option>
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153 <option value="Dark2">Dark2</option>
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154 <option value="tab10">tab10</option>
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155 <option value="tab20">tab20</option>
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156 <option value="tab20b">tab20b</option>
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157 <option value="tab20c">tab20c</option>
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158 <option value="viridis">viridis</option>
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159 <option value="plasma">plasma</option>
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160 <option value="inferno">inferno</option>
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161 <option value="magma">magma</option>
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162 <option value="terrain">terrain</option>
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163 <option value="rainbow">rainbow</option>
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164 <option value="cividis">cividis</option>
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165 </param>
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166 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
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167 <option selected="True" value="None">Selection is Optional</option>
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168 <option value="error">error</option>
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169 <option value="random">random</option>
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170 <option value="drop">drop</option>
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171 </param>
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172 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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173
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174 </inputs>
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175
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176 <outputs>
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177 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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178
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179 </outputs>
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180
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181 <help><![CDATA[
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182 Paired difference testing and boxplots
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183 ###############################################################
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184
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185 Performs paired difference testing between samples from each subject.
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186 Sample pairs may represent a typical intervention study (e.g., samples
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187 collected pre- and post-treatment), paired samples from two different
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188 timepoints (e.g., in a longitudinal study design), or identical samples
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189 receiving different treatments. This action tests whether the change in a
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190 numeric metadata value "metric" differs from zero and differs between
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191 groups (e.g., groups of subjects receiving different treatments), and
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192 produces boxplots of paired difference distributions for each group. Note
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193 that "metric" can be derived from a feature table or metadata.
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194
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195 Parameters
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196 ----------
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197 metadata : Metadata
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198 Sample metadata file containing individual_id_column.
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199 metric : Str
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200 Numerical metadata or artifact column to test.
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201 state_column : Str
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202 Metadata column containing state (e.g., Time) across which samples are
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203 paired.
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204 state_1 : Str
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205 Baseline state column value.
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206 state_2 : Str
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207 State column value to pair with baseline.
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208 individual_id_column : Str
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209 Metadata column containing subject IDs to use for pairing samples.
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210 WARNING: if replicates exist for an individual ID at either state_1 or
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211 state_2, that subject will be dropped and reported in standard output
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212 by default. Set replicate_handling="random" to instead randomly select
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213 one member.
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214 group_column : Str, optional
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215 Metadata column on which to separate groups for comparison
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216 parametric : Bool, optional
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217 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
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218 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
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219 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis'), optional
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220 Color palette to use for generating boxplots.
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221 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
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222 Choose how replicate samples are handled. If replicates are detected,
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223 "error" causes method to fail; "drop" will discard all replicated
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224 samples; "random" chooses one representative at random from among
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225 replicates.
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226 table : FeatureTable[RelativeFrequency], optional
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227 Feature table to optionally use for paired comparisons.
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228
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229 Returns
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230 -------
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231 visualization : Visualization
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232 ]]></help>
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233 <macros>
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234 <import>qiime_citation.xml</import>
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235 </macros>
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236 <expand macro="qiime_citation"/>
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237 </tool> |
