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comparison qiime2/qiime_longitudinal_pairwise-differences.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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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"
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>