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+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences" version="2018.4">
+ − 3 <description> - Paired difference testing and boxplots</description>
+ − 4 <requirements>
+ − 5 <requirement type="package" version="2018.4">qiime2</requirement>
+ − 6 </requirements>
+ − 7 <command>
+ − 8 <![CDATA[
+ − 9 qiime longitudinal pairwise-differences --p-state-column="$pstatecolumn"
+ − 10
+ − 11 #def list_dict_to_string(list_dict):
+ − 12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+ − 13 #for d in list_dict[1:]:
+ − 14 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
+ − 15 #end for
+ − 16 #return $file_list
+ − 17 #end def
+ − 18
+ − 19 --m-metadata-file=$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"
+ − 20 #if str($itable) != 'None':
+ − 21 --i-table=$itable
+ − 22 #end if
+ − 23
+ − 24 #if str($cmdconfig) != 'None':
+ − 25 --cmd-config=$cmdconfig
+ − 26 #end if
+ − 27
+ − 28 #if str($preplicatehandling) != 'None':
+ − 29 --p-replicate-handling=$preplicatehandling
+ − 30 #end if
+ − 31
+ − 32 #if $pparametric:
+ − 33 --p-parametric
+ − 34 #else
+ − 35 --p-no-parametric
+ − 36 #end if
+ − 37
+ − 38 #if str($ppalette) != 'None':
+ − 39 --p-palette=$ppalette
+ − 40 #end if
+ − 41 --o-visualization=ovisualization;
+ − 42 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
+ − 43 && cp -r out/* '$ovisualization.files_path'
+ − 44 && mv '$ovisualization.files_path/index.html' '$ovisualization'
+ − 45 ]]>
+ − 46 </command>
+ − 47 <inputs>
+ − 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"/>
+ − 49
+ − 50 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+ − 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" />
+ − 52 </repeat>
+ − 53
+ − 54 <param label="--p-group-column: Metadata column on which to separate groups for comparison [required]" name="pgroupcolumn" optional="False" type="text"/>
+ − 55 <param label="--p-metric: Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text"/>
+ − 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"/>
+ − 57
+ − 58 <param label="--p-state-1: Baseline state column value. [required]" name="pstate1" optional="False" type="text"/>
+ − 59 <param label="--p-state-2: State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text"/>
+ − 60
+ − 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"/>
+ − 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"/>
+ − 63
+ − 64 <param label="--p-palette: Color palette to use for generating
+ − 65 boxplots. [default: Set1]" name="ppalette" optional="True" type="select">
+ − 66 <option selected="True" value="None">Selection is Optional</option>
+ − 67 <option value="Accent">Accent</option>
+ − 68 <option value="tab20">tab20</option>
+ − 69 <option value="Pastel2">Pastel2</option>
+ − 70 <option value="plasma">plasma</option>
+ − 71 <option value="viridis">viridis</option>
+ − 72 <option value="rainbow">rainbow</option>
+ − 73 <option value="Pastel1">Pastel1</option>
+ − 74 <option value="inferno">inferno</option>
+ − 75 <option value="magma">magma</option>
+ − 76 <option value="tab20b">tab20b</option>
+ − 77 <option value="Set3">Set3</option>
+ − 78 <option value="Set2">Set2</option>
+ − 79 <option value="Dark2">Dark2</option>
+ − 80 <option value="Set1">Set1</option>
+ − 81 <option value="tab10">tab10</option>
+ − 82 <option value="tab20c">tab20c</option>
+ − 83 <option value="terrain">terrain</option>
+ − 84 <option value="Paired">Paired</option>
+ − 85 </param>
+ − 86
+ − 87 <param label="--p-replicate-handling: Choose how replicate samples are handled. If
+ − 88 replicates are detected, 'error' causes
+ − 89 method to fail; 'drop' will discard all
+ − 90 replicated samples; 'random' chooses one
+ − 91 representative at random from among
+ − 92 replicates. [default: error]" name="preplicatehandling" optional="True" type="select">
+ − 93 <option selected="True" value="None">Selection is Optional</option>
+ − 94 <option value="error">error</option>
+ − 95 <option value="random">random</option>
+ − 96 <option value="drop">drop</option>
+ − 97 </param>
+ − 98
+ − 99 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
+ − 100 </inputs>
+ − 101 <outputs>
+ − 102 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
+ − 103 </outputs>
+ − 104 <help>
+ − 105 <![CDATA[
+ − 106 Paired difference testing and boxplots
+ − 107 ---------------------------------------
+ − 108
+ − 109 Performs paired difference testing between samples from each subject.
+ − 110 Sample pairs may represent a typical intervention study, e.g., samples
+ − 111 collected pre- and post-treatment; paired samples from two different
+ − 112 timepoints (e.g., in a longitudinal study design), or identical samples
+ − 113 receiving different two different treatments. This action tests whether the
+ − 114 change in a numeric metadata value "metric" differs from zero and differs
+ − 115 between groups (e.g., groups of subjects receiving different treatments),
+ − 116 and produces boxplots of paired difference distributions for each group. A
+ − 117 feature table artifact is required input, though whether "metric" is
+ − 118 derived from the feature table or metadata is optional.
+ − 119
+ − 120 Parameters
+ − 121 ----------
+ − 122 table : FeatureTable[RelativeFrequency], optional
+ − 123 Feature table to optionally use for paired comparisons.
+ − 124 metadata : Metadata
+ − 125 Sample metadata file containing individual_id_column.
+ − 126 group_column : Str
+ − 127 Metadata column on which to separate groups for comparison
+ − 128 metric : Str
+ − 129 Numerical metadata or artifact column to test.
+ − 130 state_column : Str
+ − 131 Metadata column containing state (e.g., Time) across which samples are
+ − 132 paired.
+ − 133 state_1 : Str
+ − 134 Baseline state column value.
+ − 135 state_2 : Str
+ − 136 State column value to pair with baseline.
+ − 137 individual_id_column : Str
+ − 138 Metadata column containing subject IDs to use for pairing samples.
+ − 139 WARNING: if replicates exist for an individual ID at either state_1 or
+ − 140 state_2, that subject will be dropped and reported in standard output
+ − 141 by default. Set replicate_handling="random" to instead randomly select
+ − 142 one member.
+ − 143 parametric : Bool, optional
+ − 144 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
+ − 145 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
+ − 146 palette : Str % Choices({'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'inferno', 'magma', 'plasma', 'rainbow', 'tab10', 'tab20', 'tab20b', 'tab20c', 'terrain', 'viridis'}), optional
+ − 147 Color palette to use for generating boxplots.
+ − 148 replicate_handling : Str % Choices({'drop', 'error', 'random'}), optional
+ − 149 Choose how replicate samples are handled. If replicates are detected,
+ − 150 "error" causes method to fail; "drop" will discard all replicated
+ − 151 samples; "random" chooses one representative at random from among
+ − 152 replicates.
+ − 153
+ − 154 Returns
+ − 155 -------
+ − 156 visualization : Visualization
+ − 157 \
+ − 158 ]]>
+ − 159 </help>
+ − 160 </tool>
