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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" version="2019.7">
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3 <description> - Paired difference testing and boxplots</description>
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4 <requirements>
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5 <requirement type="package" version="2019.7">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime longitudinal pairwise-differences
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9
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10 --p-metric="$pmetric"
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11 --p-state-column="$pstatecolumn"
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12 --p-state-1="$pstate1"
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13 --p-state-2="$pstate2"
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4
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14
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15
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16 #if '__sq__' in str($pindividualidcolumn):
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17 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
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18 #set $pindividualidcolumn = $pindividualidcolumn_temp
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19 #end if
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20 #if str($pindividualidcolumn):
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21 --p-individual-id-column="$pindividualidcolumn"
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22 #end if
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23
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24
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0
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25
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26 #if str($itable) != 'None':
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27 --i-table=$itable
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28 #end if
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29
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30 #if str($pgroupcolumn):
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31 --p-group-column="$pgroupcolumn"
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32 #end if
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33
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34 #if $pparametric:
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35 --p-parametric
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36 #end if
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37
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38 #if str($ppalette) != 'None':
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39 --p-palette=$ppalette
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40 #end if
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41
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42 #if str($preplicatehandling) != 'None':
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43 --p-replicate-handling=$preplicatehandling
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44 #end if
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45
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46
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47 #if $input_files_mmetadatafile:
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48 #def list_dict_to_string(list_dict):
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49 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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50 #for d in list_dict[1:]:
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51 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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52 #end for
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53 #return $file_list
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54 #end def
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55 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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56 #end if
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57
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58
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59 --o-visualization=ovisualization
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60 ;
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61 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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62 && cp -r out/* '$ovisualization.files_path'
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63 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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64 ]]></command>
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65 <inputs>
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66 <param label="--p-metric: TEXT Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text"/>
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67 <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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68 <param label="--p-state-1: TEXT Baseline state column value. [required]" name="pstate1" optional="False" type="text"/>
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69 <param label="--p-state-2: TEXT State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text"/>
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70 <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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71 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to optionally use for paired comparisons. [optional]" name="itable" optional="True" type="data"/>
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72 <param label="--p-group-column: TEXT Metadata column on which to separate groups for comparison [optional]" name="pgroupcolumn" optional="True" type="text"/>
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73 <param label="--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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74 <param label="--p-palette: " name="ppalette" optional="True" type="select">
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75 <option selected="True" value="None">Selection is Optional</option>
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76 <option value="Set1">Set1</option>
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77 <option value="Set2">Set2</option>
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78 <option value="Set3">Set3</option>
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79 <option value="Pastel1">Pastel1</option>
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80 <option value="Pastel2">Pastel2</option>
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81 <option value="Paired">Paired</option>
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82 <option value="Accent">Accent</option>
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83 <option value="Dark2">Dark2</option>
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84 <option value="tab10">tab10</option>
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85 <option value="tab20">tab20</option>
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86 <option value="tab20b">tab20b</option>
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87 <option value="tab20c">tab20c</option>
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88 <option value="viridis">viridis</option>
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89 <option value="plasma">plasma</option>
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90 <option value="inferno">inferno</option>
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91 <option value="magma">magma</option>
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92 <option value="terrain">terrain</option>
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93 <option value="rainbow">rainbow</option>
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94 </param>
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95 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
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96 <option selected="True" value="None">Selection is Optional</option>
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97 <option value="error">error</option>
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98 <option value="random">random</option>
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99 <option value="drop">drop</option>
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100 </param>
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101
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102 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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103 <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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104 </repeat>
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105
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106 </inputs>
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107 <outputs>
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108 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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109 </outputs>
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110 <help><![CDATA[
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111 Paired difference testing and boxplots
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112 ######################################
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113
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114 Performs paired difference testing between samples from each subject.
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115 Sample pairs may represent a typical intervention study, e.g., samples
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116 collected pre- and post-treatment; paired samples from two different
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117 timepoints (e.g., in a longitudinal study design), or identical samples
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118 receiving different two different treatments. This action tests whether the
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119 change in a numeric metadata value "metric" differs from zero and differs
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120 between groups (e.g., groups of subjects receiving different treatments),
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121 and produces boxplots of paired difference distributions for each group. A
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122 feature table artifact is required input, though whether "metric" is
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123 derived from the feature table or metadata is optional.
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124
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125 Parameters
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126 ----------
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127 metadata : Metadata
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128 Sample metadata file containing individual_id_column.
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129 metric : Str
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130 Numerical metadata or artifact column to test.
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131 state_column : Str
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132 Metadata column containing state (e.g., Time) across which samples are
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133 paired.
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134 state_1 : Str
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135 Baseline state column value.
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136 state_2 : Str
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137 State column value to pair with baseline.
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138 individual_id_column : Str
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139 Metadata column containing subject IDs to use for pairing samples.
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140 WARNING: if replicates exist for an individual ID at either state_1 or
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141 state_2, that subject will be dropped and reported in standard output
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142 by default. Set replicate_handling="random" to instead randomly select
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143 one member.
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144 group_column : Str, optional
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145 Metadata column on which to separate groups for comparison
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146 parametric : Bool, optional
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147 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
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148 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
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149 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
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150 Color palette to use for generating boxplots.
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151 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
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152 Choose how replicate samples are handled. If replicates are detected,
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153 "error" causes method to fail; "drop" will discard all replicated
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154 samples; "random" chooses one representative at random from among
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155 replicates.
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156 table : FeatureTable[RelativeFrequency], optional
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157 Feature table to optionally use for paired comparisons.
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158
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159 Returns
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160 -------
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161 visualization : Visualization
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162 ]]></help>
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163 <macros>
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164 <import>qiime_citation.xml</import>
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165 </macros>
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166 <expand macro="qiime_citation"/>
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167 </tool>
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