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comparison qiime2/qiime_longitudinal_pairwise-differences.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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1 <?xml version="1.0" ?>
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[
9 qiime longitudinal pairwise-differences
10
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
49
50
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 = $pindividualidcolumn_temp
66 #end if
67 #if '__sq__' in str($pindividualidcolumn):
68 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
69 #set $pindividualidcolumn = $pindividualidcolumn_temp
70 #end if
71 #if '__db__' in str($pindividualidcolumn):
72 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
73 #set $pindividualidcolumn = $pindividualidcolumn_temp
74 #end if
75
76 --p-individual-id-column=$pindividualidcolumn
77
78
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 = $pgroupcolumn_temp
98 #end if
99
100 #if str($pgroupcolumn):
101 --p-group-column=$pgroupcolumn
102 #end if
103
104 #if $pparametric:
105 --p-parametric
106 #end if
107
108 #if str($ppalette) != 'None':
109 --p-palette=$ppalette
110 #end if
111
112 #if str($preplicatehandling) != 'None':
113 --p-replicate-handling=$preplicatehandling
114 #end if
115
116 --o-visualization=ovisualization
117
118 #if str($examples) != 'None':
119 --examples=$examples
120 #end if
121
122 ;
123 cp odistancematrix.qza $odistancematrix
124
125 ;
126 qiime tools export ovisualization.qzv --output-path out
127 && mkdir -p '$ovisualization.files_path'
128 && cp -r out/* '$ovisualization.files_path'
129 && mv '$ovisualization.files_path/index.html' '$ovisualization'
130
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>
175
176 <outputs>
177 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
178
179 </outputs>
180
181 <help><![CDATA[
182 Paired difference testing and boxplots
183 ###############################################################
184
185 Performs paired difference testing between samples from each subject.
186 Sample pairs may represent a typical intervention study (e.g., samples
187 collected pre- and post-treatment), paired samples from two different
188 timepoints (e.g., in a longitudinal study design), or identical samples
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.
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.
219 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis'), optional
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
232 ]]></help>
233 <macros>
234 <import>qiime_citation.xml</import>
235 </macros>
236 <expand macro="qiime_citation"/>
237 </tool>