|
0
|
1 <?xml version="1.0" ?>
|
|
14
|
2 <tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences"
|
|
|
3 version="2020.8">
|
|
|
4 <description>Paired difference testing and boxplots</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
0
|
9 qiime longitudinal pairwise-differences
|
|
|
10
|
|
14
|
11 #if str($itable) != 'None':
|
|
|
12 --i-table=$itable
|
|
|
13 #end if
|
|
|
14 # if $input_files_mmetadatafile:
|
|
|
15 # def list_dict_to_string(list_dict):
|
|
|
16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
17 # for d in list_dict[1:]:
|
|
|
18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
|
19 # end for
|
|
|
20 # return $file_list
|
|
|
21 # end def
|
|
|
22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
|
|
|
23 # end if
|
|
|
24
|
|
|
25 --p-metric=$pmetric
|
|
|
26
|
|
|
27 #if '__ob__' in str($pstatecolumn):
|
|
|
28 #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
|
|
|
29 #set $pstatecolumn = $pstatecolumn_temp
|
|
|
30 #end if
|
|
|
31 #if '__cb__' in str($pstatecolumn):
|
|
|
32 #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
|
|
|
33 #set $pstatecolumn = $pstatecolumn_temp
|
|
|
34 #end if
|
|
|
35 #if 'X' in str($pstatecolumn):
|
|
|
36 #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
|
|
|
37 #set $pstatecolumn = $pstatecolumn_temp
|
|
|
38 #end if
|
|
|
39 #if '__sq__' in str($pstatecolumn):
|
|
|
40 #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
|
|
|
41 #set $pstatecolumn = $pstatecolumn_temp
|
|
|
42 #end if
|
|
|
43 #if '__db__' in str($pstatecolumn):
|
|
|
44 #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
|
|
|
45 #set $pstatecolumn = $pstatecolumn_temp
|
|
|
46 #end if
|
|
|
47
|
|
|
48 --p-state-column=$pstatecolumn
|
|
4
|
49
|
|
|
50
|
|
14
|
51 --p-state-1=$pstate1
|
|
|
52
|
|
|
53 --p-state-2=$pstate2
|
|
|
54
|
|
|
55 #if '__ob__' in str($pindividualidcolumn):
|
|
|
56 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
|
|
|
57 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
58 #end if
|
|
|
59 #if '__cb__' in str($pindividualidcolumn):
|
|
|
60 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
|
|
|
61 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
62 #end if
|
|
|
63 #if 'X' in str($pindividualidcolumn):
|
|
|
64 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
|
|
|
65 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
66 #end if
|
|
4
|
67 #if '__sq__' in str($pindividualidcolumn):
|
|
|
68 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
|
|
|
69 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
|
70 #end if
|
|
14
|
71 #if '__db__' in str($pindividualidcolumn):
|
|
|
72 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
|
|
|
73 #set $pindividualidcolumn = $pindividualidcolumn_temp
|
|
4
|
74 #end if
|
|
|
75
|
|
14
|
76 --p-individual-id-column=$pindividualidcolumn
|
|
4
|
77
|
|
0
|
78
|
|
14
|
79 #if '__ob__' in str($pgroupcolumn):
|
|
|
80 #set $pgroupcolumn_temp = $pgroupcolumn.replace('__ob__', '[')
|
|
|
81 #set $pgroupcolumn = $pgroupcolumn_temp
|
|
|
82 #end if
|
|
|
83 #if '__cb__' in str($pgroupcolumn):
|
|
|
84 #set $pgroupcolumn_temp = $pgroupcolumn.replace('__cb__', ']')
|
|
|
85 #set $pgroupcolumn = $pgroupcolumn_temp
|
|
|
86 #end if
|
|
|
87 #if 'X' in str($pgroupcolumn):
|
|
|
88 #set $pgroupcolumn_temp = $pgroupcolumn.replace('X', '\\')
|
|
|
89 #set $pgroupcolumn = $pgroupcolumn_temp
|
|
|
90 #end if
|
|
|
91 #if '__sq__' in str($pgroupcolumn):
|
|
|
92 #set $pgroupcolumn_temp = $pgroupcolumn.replace('__sq__', "'")
|
|
|
93 #set $pgroupcolumn = $pgroupcolumn_temp
|
|
|
94 #end if
|
|
|
95 #if '__db__' in str($pgroupcolumn):
|
|
|
96 #set $pgroupcolumn_temp = $pgroupcolumn.replace('__db__', '"')
|
|
|
97 #set $pgroupcolumn = $pgroupcolumn_temp
|
|
0
|
98 #end if
|
|
|
99
|
|
|
100 #if str($pgroupcolumn):
|
|
14
|
101 --p-group-column=$pgroupcolumn
|
|
0
|
102 #end if
|
|
|
103
|
|
|
104 #if $pparametric:
|
|
|
105 --p-parametric
|
|
|
106 #end if
|
|
|
107
|
|
|
108 #if str($ppalette) != 'None':
|
|
14
|
109 --p-palette=$ppalette
|
|
0
|
110 #end if
|
|
|
111
|
|
|
112 #if str($preplicatehandling) != 'None':
|
|
14
|
113 --p-replicate-handling=$preplicatehandling
|
|
0
|
114 #end if
|
|
|
115
|
|
|
116 --o-visualization=ovisualization
|
|
14
|
117
|
|
|
118 #if str($examples) != 'None':
|
|
|
119 --examples=$examples
|
|
|
120 #end if
|
|
|
121
|
|
0
|
122 ;
|
|
14
|
123 cp odistancematrix.qza $odistancematrix
|
|
|
124
|
|
|
125 ;
|
|
|
126 qiime tools export ovisualization.qzv --output-path out
|
|
|
127 && mkdir -p '$ovisualization.files_path'
|
|
0
|
128 && cp -r out/* '$ovisualization.files_path'
|
|
14
|
129 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
0
|
130
|
|
14
|
131 ]]></command>
|
|
|
132 <inputs>
|
|
|
133 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to optionally use for paired comparisons. [optional]" name="itable" optional="False" type="data" />
|
|
|
134 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
|
|
|
135 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata file containing arguments will be individual-id-column. merged) [required]" name="additional_input" optional="False" type="data" />
|
|
|
136 </repeat>
|
|
|
137 <param label="--p-metric: TEXT Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text" />
|
|
|
138 <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" />
|
|
|
139 <param label="--p-state-1: TEXT Baseline state column value. [required]" name="pstate1" optional="False" type="text" />
|
|
|
140 <param label="--p-state-2: TEXT State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text" />
|
|
|
141 <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" />
|
|
|
142 <param label="--p-group-column: TEXT Metadata column on which to separate groups for comparison [optional]" name="pgroupcolumn" optional="False" type="text" />
|
|
|
143 <param label="--p-parametric: --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" />
|
|
|
144 <param label="--p-palette: " name="ppalette" optional="True" type="select">
|
|
|
145 <option selected="True" value="None">Selection is Optional</option>
|
|
|
146 <option value="Set1">Set1</option>
|
|
|
147 <option value="Set2">Set2</option>
|
|
|
148 <option value="Set3">Set3</option>
|
|
|
149 <option value="Pastel1">Pastel1</option>
|
|
|
150 <option value="Pastel2">Pastel2</option>
|
|
|
151 <option value="Paired">Paired</option>
|
|
|
152 <option value="Accent">Accent</option>
|
|
|
153 <option value="Dark2">Dark2</option>
|
|
|
154 <option value="tab10">tab10</option>
|
|
|
155 <option value="tab20">tab20</option>
|
|
|
156 <option value="tab20b">tab20b</option>
|
|
|
157 <option value="tab20c">tab20c</option>
|
|
|
158 <option value="viridis">viridis</option>
|
|
|
159 <option value="plasma">plasma</option>
|
|
|
160 <option value="inferno">inferno</option>
|
|
|
161 <option value="magma">magma</option>
|
|
|
162 <option value="terrain">terrain</option>
|
|
|
163 <option value="rainbow">rainbow</option>
|
|
|
164 <option value="cividis">cividis</option>
|
|
|
165 </param>
|
|
|
166 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
|
|
|
167 <option selected="True" value="None">Selection is Optional</option>
|
|
|
168 <option value="error">error</option>
|
|
|
169 <option value="random">random</option>
|
|
|
170 <option value="drop">drop</option>
|
|
|
171 </param>
|
|
|
172 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
173
|
|
|
174 </inputs>
|
|
0
|
175
|
|
14
|
176 <outputs>
|
|
|
177 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
|
|
|
178
|
|
|
179 </outputs>
|
|
|
180
|
|
|
181 <help><![CDATA[
|
|
0
|
182 Paired difference testing and boxplots
|
|
14
|
183 ###############################################################
|
|
0
|
184
|
|
|
185 Performs paired difference testing between samples from each subject.
|
|
14
|
186 Sample pairs may represent a typical intervention study (e.g., samples
|
|
|
187 collected pre- and post-treatment), paired samples from two different
|
|
0
|
188 timepoints (e.g., in a longitudinal study design), or identical samples
|
|
14
|
189 receiving different treatments. This action tests whether the change in a
|
|
|
190 numeric metadata value "metric" differs from zero and differs between
|
|
|
191 groups (e.g., groups of subjects receiving different treatments), and
|
|
|
192 produces boxplots of paired difference distributions for each group. Note
|
|
|
193 that "metric" can be derived from a feature table or metadata.
|
|
0
|
194
|
|
|
195 Parameters
|
|
|
196 ----------
|
|
|
197 metadata : Metadata
|
|
|
198 Sample metadata file containing individual_id_column.
|
|
|
199 metric : Str
|
|
|
200 Numerical metadata or artifact column to test.
|
|
|
201 state_column : Str
|
|
|
202 Metadata column containing state (e.g., Time) across which samples are
|
|
|
203 paired.
|
|
|
204 state_1 : Str
|
|
|
205 Baseline state column value.
|
|
|
206 state_2 : Str
|
|
|
207 State column value to pair with baseline.
|
|
|
208 individual_id_column : Str
|
|
|
209 Metadata column containing subject IDs to use for pairing samples.
|
|
|
210 WARNING: if replicates exist for an individual ID at either state_1 or
|
|
|
211 state_2, that subject will be dropped and reported in standard output
|
|
|
212 by default. Set replicate_handling="random" to instead randomly select
|
|
|
213 one member.
|
|
|
214 group_column : Str, optional
|
|
|
215 Metadata column on which to separate groups for comparison
|
|
|
216 parametric : Bool, optional
|
|
|
217 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
|
|
|
218 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
|
|
14
|
219 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis'), optional
|
|
0
|
220 Color palette to use for generating boxplots.
|
|
|
221 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
|
|
|
222 Choose how replicate samples are handled. If replicates are detected,
|
|
|
223 "error" causes method to fail; "drop" will discard all replicated
|
|
|
224 samples; "random" chooses one representative at random from among
|
|
|
225 replicates.
|
|
|
226 table : FeatureTable[RelativeFrequency], optional
|
|
|
227 Feature table to optionally use for paired comparisons.
|
|
|
228
|
|
|
229 Returns
|
|
|
230 -------
|
|
|
231 visualization : Visualization
|
|
14
|
232 ]]></help>
|
|
|
233 <macros>
|
|
0
|
234 <import>qiime_citation.xml</import>
|
|
14
|
235 </macros>
|
|
|
236 <expand macro="qiime_citation"/>
|
|
|
237 </tool> |
