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