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