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

Uploaded
author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
parents
children 914fa4daf16a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Paired difference testing and boxplots</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime longitudinal pairwise-differences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --p-metric="$pmetric"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --p-state-column="$pstatecolumn"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12 --p-state-1="$pstate1"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 --p-state-2="$pstate2"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 --p-individual-id-column="$pindividualidcolumn"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 #if str($itable) != 'None':
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 --i-table=$itable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 #if str($pgroupcolumn):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 --p-group-column="$pgroupcolumn"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 #if $pparametric:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 --p-parametric
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 #if str($ppalette) != 'None':
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 --p-palette=$ppalette
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 #if str($preplicatehandling) != 'None':
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 --p-replicate-handling=$preplicatehandling
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 #if $input_files_mmetadatafile:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 #def list_dict_to_string(list_dict):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 #for d in list_dict[1:]:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 #end for
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 #return $file_list
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 #end def
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 --o-visualization=ovisualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 && cp -r out/* '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 && mv '$ovisualization.files_path/index.html' '$ovisualization';
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 <param label="--p-metric: TEXT Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 <param label="--p-state-1: TEXT Baseline state column value. [required]" name="pstate1" optional="False" type="text"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 <param label="--p-state-2: TEXT State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 <param label="--p-group-column: TEXT Metadata column on which to separate groups for comparison [optional]" name="pgroupcolumn" optional="True" type="text"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 <param label="--p-palette: " name="ppalette" optional="True" type="select">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 <option selected="True" value="None">Selection is Optional</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 <option value="Set1">Set1</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 <option value="Set2">Set2</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 <option value="Set3">Set3</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 <option value="Pastel1">Pastel1</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 <option value="Pastel2">Pastel2</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 <option value="Paired">Paired</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72 <option value="Accent">Accent</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73 <option value="Dark2">Dark2</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 <option value="tab10">tab10</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75 <option value="tab20">tab20</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76 <option value="tab20b">tab20b</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
77 <option value="tab20c">tab20c</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
78 <option value="viridis">viridis</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
79 <option value="plasma">plasma</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
80 <option value="inferno">inferno</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
81 <option value="magma">magma</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
82 <option value="terrain">terrain</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
83 <option value="rainbow">rainbow</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
84 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
85 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
86 <option selected="True" value="None">Selection is Optional</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
87 <option value="error">error</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
88 <option value="random">random</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
89 <option value="drop">drop</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
90 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
91
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
92 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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" />
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
94 </repeat>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
95
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
96 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
97 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
98 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
99 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
100 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
101 Paired difference testing and boxplots
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
102 ######################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
103
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
104 Performs paired difference testing between samples from each subject.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
105 Sample pairs may represent a typical intervention study, e.g., samples
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
106 collected pre- and post-treatment; paired samples from two different
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
107 timepoints (e.g., in a longitudinal study design), or identical samples
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
108 receiving different two different treatments. This action tests whether the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
109 change in a numeric metadata value "metric" differs from zero and differs
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
110 between groups (e.g., groups of subjects receiving different treatments),
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
111 and produces boxplots of paired difference distributions for each group. A
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
112 feature table artifact is required input, though whether "metric" is
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
113 derived from the feature table or metadata is optional.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
114
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
115 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
116 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
117 metadata : Metadata
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
118 Sample metadata file containing individual_id_column.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
119 metric : Str
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
120 Numerical metadata or artifact column to test.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
121 state_column : Str
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
122 Metadata column containing state (e.g., Time) across which samples are
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
123 paired.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
124 state_1 : Str
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
125 Baseline state column value.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
126 state_2 : Str
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
127 State column value to pair with baseline.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
128 individual_id_column : Str
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
129 Metadata column containing subject IDs to use for pairing samples.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
130 WARNING: if replicates exist for an individual ID at either state_1 or
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
131 state_2, that subject will be dropped and reported in standard output
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
132 by default. Set replicate_handling="random" to instead randomly select
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
133 one member.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
134 group_column : Str, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
135 Metadata column on which to separate groups for comparison
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
136 parametric : Bool, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
137 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
138 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
139 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
140 Color palette to use for generating boxplots.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
141 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
142 Choose how replicate samples are handled. If replicates are detected,
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
143 "error" causes method to fail; "drop" will discard all replicated
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
144 samples; "random" chooses one representative at random from among
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
145 replicates.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
146 table : FeatureTable[RelativeFrequency], optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
147 Feature table to optionally use for paired comparisons.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
148
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
149 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
150 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
151 visualization : Visualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
152 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
153 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
154 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
155 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
156 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
157 </tool>