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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="2018.4">
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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="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 longitudinal pairwise-differences --p-state-column="$pstatecolumn"
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10
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11 #def list_dict_to_string(list_dict):
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12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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13 #for d in list_dict[1:]:
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14 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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15 #end for
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16 #return $file_list
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17 #end def
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18
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19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-group-column="$pgroupcolumn" --p-individual-id-column="$pindividualidcolumn" --p-state-1="$pstate1" --p-state-2="$pstate2" --p-metric="$pmetric"
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20 #if str($itable) != 'None':
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21 --i-table=$itable
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22 #end if
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23
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24 #if str($cmdconfig) != 'None':
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25 --cmd-config=$cmdconfig
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26 #end if
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27
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28 #if str($preplicatehandling) != 'None':
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29 --p-replicate-handling=$preplicatehandling
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30 #end if
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31
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32 #if $pparametric:
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33 --p-parametric
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34 #else
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35 --p-no-parametric
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36 #end if
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37
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38 #if str($ppalette) != 'None':
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39 --p-palette=$ppalette
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40 #end if
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41 --o-visualization=ovisualization;
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42 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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43 && cp -r out/* '$ovisualization.files_path'
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44 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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45 ]]>
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46 </command>
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47 <inputs>
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48 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[RelativeFrequency] Feature table to optionally use for paired comparisons. [optional]" name="itable" optional="True" type="data"/>
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49
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50 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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51 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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52 </repeat>
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53
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54 <param label="--p-group-column: Metadata column on which to separate groups for comparison [required]" name="pgroupcolumn" optional="False" type="text"/>
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55 <param label="--p-metric: Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text"/>
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56 <param label="--p-state-column: Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text"/>
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57
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58 <param label="--p-state-1: Baseline state column value. [required]" name="pstate1" optional="False" type="text"/>
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59 <param label="--p-state-2: State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text"/>
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60
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61 <param label="--p-individual-id-column: 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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62 <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" checked="False" type="boolean"/>
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63
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64 <param label="--p-palette: Color palette to use for generating
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65 boxplots. [default: Set1]" name="ppalette" optional="True" type="select">
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66 <option selected="True" value="None">Selection is Optional</option>
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67 <option value="Accent">Accent</option>
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68 <option value="tab20">tab20</option>
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69 <option value="Pastel2">Pastel2</option>
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70 <option value="plasma">plasma</option>
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71 <option value="viridis">viridis</option>
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72 <option value="rainbow">rainbow</option>
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73 <option value="Pastel1">Pastel1</option>
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74 <option value="inferno">inferno</option>
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75 <option value="magma">magma</option>
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76 <option value="tab20b">tab20b</option>
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77 <option value="Set3">Set3</option>
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78 <option value="Set2">Set2</option>
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79 <option value="Dark2">Dark2</option>
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80 <option value="Set1">Set1</option>
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81 <option value="tab10">tab10</option>
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82 <option value="tab20c">tab20c</option>
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83 <option value="terrain">terrain</option>
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84 <option value="Paired">Paired</option>
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85 </param>
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86
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87 <param label="--p-replicate-handling: Choose how replicate samples are handled. If
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88 replicates are detected, 'error' causes
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89 method to fail; 'drop' will discard all
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90 replicated samples; 'random' chooses one
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91 representative at random from among
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92 replicates. [default: error]" name="preplicatehandling" optional="True" type="select">
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93 <option selected="True" value="None">Selection is Optional</option>
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94 <option value="error">error</option>
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95 <option value="random">random</option>
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96 <option value="drop">drop</option>
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97 </param>
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98
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99 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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100 </inputs>
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101 <outputs>
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102 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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103 </outputs>
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104 <help>
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105 <![CDATA[
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106 Paired difference testing and boxplots
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107 ---------------------------------------
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108
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109 Performs paired difference testing between samples from each subject.
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110 Sample pairs may represent a typical intervention study, e.g., samples
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111 collected pre- and post-treatment; paired samples from two different
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112 timepoints (e.g., in a longitudinal study design), or identical samples
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113 receiving different two different treatments. This action tests whether the
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114 change in a numeric metadata value "metric" differs from zero and differs
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115 between groups (e.g., groups of subjects receiving different treatments),
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116 and produces boxplots of paired difference distributions for each group. A
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117 feature table artifact is required input, though whether "metric" is
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118 derived from the feature table or metadata is optional.
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119
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120 Parameters
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121 ----------
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122 table : FeatureTable[RelativeFrequency], optional
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123 Feature table to optionally use for paired comparisons.
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124 metadata : Metadata
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125 Sample metadata file containing individual_id_column.
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126 group_column : Str
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127 Metadata column on which to separate groups for comparison
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128 metric : Str
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129 Numerical metadata or artifact column to test.
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130 state_column : Str
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131 Metadata column containing state (e.g., Time) across which samples are
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132 paired.
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133 state_1 : Str
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134 Baseline state column value.
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135 state_2 : Str
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136 State column value to pair with baseline.
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137 individual_id_column : Str
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138 Metadata column containing subject IDs to use for pairing samples.
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139 WARNING: if replicates exist for an individual ID at either state_1 or
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140 state_2, that subject will be dropped and reported in standard output
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141 by default. Set replicate_handling="random" to instead randomly select
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142 one member.
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143 parametric : Bool, optional
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144 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
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145 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
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146 palette : Str % Choices({'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'inferno', 'magma', 'plasma', 'rainbow', 'tab10', 'tab20', 'tab20b', 'tab20c', 'terrain', 'viridis'}), optional
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147 Color palette to use for generating boxplots.
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148 replicate_handling : Str % Choices({'drop', 'error', 'random'}), optional
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149 Choose how replicate samples are handled. If replicates are detected,
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150 "error" causes method to fail; "drop" will discard all replicated
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151 samples; "random" chooses one representative at random from among
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152 replicates.
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153
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154 Returns
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155 -------
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156 visualization : Visualization
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157 \
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158 ]]>
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159 </help>
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160 </tool>
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