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+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences" version="2019.4">
+ − 3 <description> - Paired difference testing and boxplots</description>
+ − 4 <requirements>
+ − 5 <requirement type="package" version="2019.4">qiime2</requirement>
+ − 6 </requirements>
+ − 7 <command><![CDATA[
+ − 8 qiime longitudinal pairwise-differences
+ − 9
+ − 10 --p-metric="$pmetric"
+ − 11 --p-state-column="$pstatecolumn"
+ − 12 --p-state-1="$pstate1"
+ − 13 --p-state-2="$pstate2"
4
+ − 14
+ − 15
+ − 16 #if '__sq__' in str($pindividualidcolumn):
+ − 17 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
+ − 18 #set $pindividualidcolumn = $pindividualidcolumn_temp
+ − 19 #end if
+ − 20 #if str($pindividualidcolumn):
+ − 21 --p-individual-id-column="$pindividualidcolumn"
+ − 22 #end if
+ − 23
+ − 24
2
+ − 25
+ − 26 #if str($itable) != 'None':
+ − 27 --i-table=$itable
+ − 28 #end if
+ − 29
+ − 30 #if str($pgroupcolumn):
+ − 31 --p-group-column="$pgroupcolumn"
+ − 32 #end if
+ − 33
+ − 34 #if $pparametric:
+ − 35 --p-parametric
+ − 36 #end if
+ − 37
+ − 38 #if str($ppalette) != 'None':
+ − 39 --p-palette=$ppalette
+ − 40 #end if
+ − 41
+ − 42 #if str($preplicatehandling) != 'None':
+ − 43 --p-replicate-handling=$preplicatehandling
+ − 44 #end if
+ − 45
+ − 46
+ − 47 #if $input_files_mmetadatafile:
+ − 48 #def list_dict_to_string(list_dict):
+ − 49 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+ − 50 #for d in list_dict[1:]:
+ − 51 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
+ − 52 #end for
+ − 53 #return $file_list
+ − 54 #end def
+ − 55 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+ − 56 #end if
+ − 57
+ − 58
+ − 59 --o-visualization=ovisualization
+ − 60 ;
+ − 61 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
+ − 62 && cp -r out/* '$ovisualization.files_path'
+ − 63 && mv '$ovisualization.files_path/index.html' '$ovisualization';
+ − 64 ]]></command>
+ − 65 <inputs>
+ − 66 <param label="--p-metric: TEXT Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text"/>
+ − 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"/>
+ − 68 <param label="--p-state-1: TEXT Baseline state column value. [required]" name="pstate1" optional="False" type="text"/>
+ − 69 <param label="--p-state-2: TEXT State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text"/>
+ − 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"/>
+ − 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"/>
+ − 72 <param label="--p-group-column: TEXT Metadata column on which to separate groups for comparison [optional]" name="pgroupcolumn" optional="True" type="text"/>
+ − 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"/>
+ − 74 <param label="--p-palette: " name="ppalette" optional="True" type="select">
+ − 75 <option selected="True" value="None">Selection is Optional</option>
+ − 76 <option value="Set1">Set1</option>
+ − 77 <option value="Set2">Set2</option>
+ − 78 <option value="Set3">Set3</option>
+ − 79 <option value="Pastel1">Pastel1</option>
+ − 80 <option value="Pastel2">Pastel2</option>
+ − 81 <option value="Paired">Paired</option>
+ − 82 <option value="Accent">Accent</option>
+ − 83 <option value="Dark2">Dark2</option>
+ − 84 <option value="tab10">tab10</option>
+ − 85 <option value="tab20">tab20</option>
+ − 86 <option value="tab20b">tab20b</option>
+ − 87 <option value="tab20c">tab20c</option>
+ − 88 <option value="viridis">viridis</option>
+ − 89 <option value="plasma">plasma</option>
+ − 90 <option value="inferno">inferno</option>
+ − 91 <option value="magma">magma</option>
+ − 92 <option value="terrain">terrain</option>
+ − 93 <option value="rainbow">rainbow</option>
+ − 94 </param>
+ − 95 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
+ − 96 <option selected="True" value="None">Selection is Optional</option>
+ − 97 <option value="error">error</option>
+ − 98 <option value="random">random</option>
+ − 99 <option value="drop">drop</option>
+ − 100 </param>
+ − 101
+ − 102 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+ − 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" />
+ − 104 </repeat>
+ − 105
+ − 106 </inputs>
+ − 107 <outputs>
+ − 108 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
+ − 109 </outputs>
+ − 110 <help><![CDATA[
+ − 111 Paired difference testing and boxplots
+ − 112 ######################################
+ − 113
+ − 114 Performs paired difference testing between samples from each subject.
+ − 115 Sample pairs may represent a typical intervention study, e.g., samples
+ − 116 collected pre- and post-treatment; paired samples from two different
+ − 117 timepoints (e.g., in a longitudinal study design), or identical samples
+ − 118 receiving different two different treatments. This action tests whether the
+ − 119 change in a numeric metadata value "metric" differs from zero and differs
+ − 120 between groups (e.g., groups of subjects receiving different treatments),
+ − 121 and produces boxplots of paired difference distributions for each group. A
+ − 122 feature table artifact is required input, though whether "metric" is
+ − 123 derived from the feature table or metadata is optional.
+ − 124
+ − 125 Parameters
+ − 126 ----------
+ − 127 metadata : Metadata
+ − 128 Sample metadata file containing individual_id_column.
+ − 129 metric : Str
+ − 130 Numerical metadata or artifact column to test.
+ − 131 state_column : Str
+ − 132 Metadata column containing state (e.g., Time) across which samples are
+ − 133 paired.
+ − 134 state_1 : Str
+ − 135 Baseline state column value.
+ − 136 state_2 : Str
+ − 137 State column value to pair with baseline.
+ − 138 individual_id_column : Str
+ − 139 Metadata column containing subject IDs to use for pairing samples.
+ − 140 WARNING: if replicates exist for an individual ID at either state_1 or
+ − 141 state_2, that subject will be dropped and reported in standard output
+ − 142 by default. Set replicate_handling="random" to instead randomly select
+ − 143 one member.
+ − 144 group_column : Str, optional
+ − 145 Metadata column on which to separate groups for comparison
+ − 146 parametric : Bool, optional
+ − 147 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
+ − 148 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
+ − 149 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
+ − 150 Color palette to use for generating boxplots.
+ − 151 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
+ − 152 Choose how replicate samples are handled. If replicates are detected,
+ − 153 "error" causes method to fail; "drop" will discard all replicated
+ − 154 samples; "random" chooses one representative at random from among
+ − 155 replicates.
+ − 156 table : FeatureTable[RelativeFrequency], optional
+ − 157 Feature table to optionally use for paired comparisons.
+ − 158
+ − 159 Returns
+ − 160 -------
+ − 161 visualization : Visualization
+ − 162 ]]></help>
+ − 163 <macros>
+ − 164 <import>qiime_citation.xml</import>
+ − 165 </macros>
+ − 166 <expand macro="qiime_citation"/>
+ − 167 </tool>
