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comparison qiime2/qiime_longitudinal_pairwise-distances.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_pairwise-distances" name="qiime longitudinal pairwise-distances" version="2019.7"> 2 <tool id="qiime_longitudinal_pairwise-distances" name="qiime longitudinal pairwise-distances"
3 <description> - Paired pairwise distance testing and boxplots</description> 3 version="2020.8">
4 <requirements> 4 <description>Paired pairwise distance testing and boxplots</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime longitudinal pairwise-distances 9 qiime longitudinal pairwise-distances
9 10
10 --i-distance-matrix=$idistancematrix 11 --i-distance-matrix=$idistancematrix
11 --p-group-column="$pgroupcolumn" 12 # if $input_files_mmetadatafile:
12 --p-state-column="$pstatecolumn" 13 # def list_dict_to_string(list_dict):
13 --p-state-1="$pstate1" 14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
14 --p-state-2="$pstate2" 15 # for d in list_dict[1:]:
15 16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
16 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 = $pindividualidcolumn_temp
86 #end if
17 #if '__sq__' in str($pindividualidcolumn): 87 #if '__sq__' in str($pindividualidcolumn):
18 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'") 88 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
19 #set $pindividualidcolumn = $pindividualidcolumn_temp 89 #set $pindividualidcolumn = $pindividualidcolumn_temp
20 #end if 90 #end if
21 #if str($pindividualidcolumn): 91 #if '__db__' in str($pindividualidcolumn):
22 --p-individual-id-column="$pindividualidcolumn" 92 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
23 #end if 93 #set $pindividualidcolumn = $pindividualidcolumn_temp
24 94 #end if
95
96 --p-individual-id-column=$pindividualidcolumn
25 97
26 98
27 #if $pparametric: 99 #if $pparametric:
28 --p-parametric 100 --p-parametric
29 #end if 101 #end if
30 102
31 #if str($ppalette) != 'None': 103 #if str($ppalette) != 'None':
32 --p-palette=$ppalette 104 --p-palette=$ppalette
33 #end if 105 #end if
34 106
35 #if str($preplicatehandling) != 'None': 107 #if str($preplicatehandling) != 'None':
36 --p-replicate-handling=$preplicatehandling 108 --p-replicate-handling=$preplicatehandling
37 #end if 109 #end if
38
39
40 #if $input_files_mmetadatafile:
41 #def list_dict_to_string(list_dict):
42 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
43 #for d in list_dict[1:]:
44 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
45 #end for
46 #return $file_list
47 #end def
48 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
49 #end if
50
51 110
52 --o-visualization=ovisualization 111 --o-visualization=ovisualization
112
113 #if str($examples) != 'None':
114 --examples=$examples
115 #end if
116
53 ; 117 ;
54 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 118 cp odistancematrix.qza $odistancematrix
119
120 ;
121 qiime tools export ovisualization.qzv --output-path out
122 && mkdir -p '$ovisualization.files_path'
55 && cp -r out/* '$ovisualization.files_path' 123 && cp -r out/* '$ovisualization.files_path'
56 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 124 && mv '$ovisualization.files_path/index.html' '$ovisualization'
57 ]]></command> 125
58 <inputs> 126 ;
59 <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"/> 127 qiime tools export ovisualization.qzv --output-path out
60 <param label="--p-group-column: TEXT Metadata column on which to separate groups for comparison [required]" name="pgroupcolumn" optional="False" type="text"/> 128 && mkdir -p '$ovisualization.files_path'
61 <param label="--p-state-column: TEXT Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text"/> 129 && cp -r out/* '$ovisualization.files_path'
62 <param label="--p-state-1: TEXT Baseline state column value. [required]" name="pstate1" optional="False" type="text"/> 130 && mv '$ovisualization.files_path/index.html' '$ovisualization'
63 <param label="--p-state-2: TEXT State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text"/> 131
64 <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"/> 132 ]]></command>
65 <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"/> 133 <inputs>
66 <param label="--p-palette: " name="ppalette" optional="True" type="select"> 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" />
67 <option selected="True" value="None">Selection is Optional</option> 135 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
68 <option value="Set1">Set1</option> 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" />
69 <option value="Set2">Set2</option> 137 </repeat>
70 <option value="Set3">Set3</option> 138 <param label="--p-group-column: TEXT Metadata column on which to separate groups for comparison [required]" name="pgroupcolumn" optional="False" type="text" />
71 <option value="Pastel1">Pastel1</option> 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" />
72 <option value="Pastel2">Pastel2</option> 140 <param label="--p-state-1: TEXT Baseline state column value. [required]" name="pstate1" optional="False" type="text" />
73 <option value="Paired">Paired</option> 141 <param label="--p-state-2: TEXT State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text" />
74 <option value="Accent">Accent</option> 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" />
75 <option value="Dark2">Dark2</option> 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" />
76 <option value="tab10">tab10</option> 144 <param label="--p-palette: " name="ppalette" optional="True" type="select">
77 <option value="tab20">tab20</option> 145 <option selected="True" value="None">Selection is Optional</option>
78 <option value="tab20b">tab20b</option> 146 <option value="Set1">Set1</option>
79 <option value="tab20c">tab20c</option> 147 <option value="Set2">Set2</option>
80 <option value="viridis">viridis</option> 148 <option value="Set3">Set3</option>
81 <option value="plasma">plasma</option> 149 <option value="Pastel1">Pastel1</option>
82 <option value="inferno">inferno</option> 150 <option value="Pastel2">Pastel2</option>
83 <option value="magma">magma</option> 151 <option value="Paired">Paired</option>
84 <option value="terrain">terrain</option> 152 <option value="Accent">Accent</option>
85 <option value="rainbow">rainbow</option> 153 <option value="Dark2">Dark2</option>
86 </param> 154 <option value="tab10">tab10</option>
87 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select"> 155 <option value="tab20">tab20</option>
88 <option selected="True" value="None">Selection is Optional</option> 156 <option value="tab20b">tab20b</option>
89 <option value="error">error</option> 157 <option value="tab20c">tab20c</option>
90 <option value="random">random</option> 158 <option value="viridis">viridis</option>
91 <option value="drop">drop</option> 159 <option value="plasma">plasma</option>
92 </param> 160 <option value="inferno">inferno</option>
93 161 <option value="magma">magma</option>
94 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> 162 <option value="terrain">terrain</option>
95 <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" /> 163 <option value="rainbow">rainbow</option>
96 </repeat> 164 <option value="cividis">cividis</option>
97 </inputs> 165 </param>
98 <outputs> 166 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
99 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 167 <option selected="True" value="None">Selection is Optional</option>
100 </outputs> 168 <option value="error">error</option>
101 <help><![CDATA[ 169 <option value="random">random</option>
170 <option value="drop">drop</option>
171 </param>
172 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
173
174 </inputs>
175
176 <outputs>
177 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
178
179 </outputs>
180
181 <help><![CDATA[
102 Paired pairwise distance testing and boxplots 182 Paired pairwise distance testing and boxplots
103 ############################################# 183 ###############################################################
104 184
105 Performs pairwise distance testing between sample pairs from each subject. 185 Performs pairwise distance testing between sample pairs from each subject.
106 Sample pairs may represent a typical intervention study, e.g., samples 186 Sample pairs may represent a typical intervention study, e.g., samples
107 collected pre- and post-treatment; paired samples from two different 187 collected pre- and post-treatment; paired samples from two different
108 timepoints (e.g., in a longitudinal study design), or identical samples 188 timepoints (e.g., in a longitudinal study design), or identical samples
133 by default. Set replicate_handling="random" to instead randomly select 213 by default. Set replicate_handling="random" to instead randomly select
134 one member. 214 one member.
135 parametric : Bool, optional 215 parametric : Bool, optional
136 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal- 216 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
137 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests. 217 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
138 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional 218 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis'), optional
139 Color palette to use for generating boxplots. 219 Color palette to use for generating boxplots.
140 replicate_handling : Str % Choices('error', 'random', 'drop'), optional 220 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
141 Choose how replicate samples are handled. If replicates are detected, 221 Choose how replicate samples are handled. If replicates are detected,
142 "error" causes method to fail; "drop" will discard all replicated 222 "error" causes method to fail; "drop" will discard all replicated
143 samples; "random" chooses one representative at random from among 223 samples; "random" chooses one representative at random from among
144 replicates. 224 replicates.
145 225
146 Returns 226 Returns
147 ------- 227 -------
148 visualization : Visualization 228 visualization : Visualization
149 ]]></help> 229 ]]></help>
150 <macros> 230 <macros>
151 <import>qiime_citation.xml</import> 231 <import>qiime_citation.xml</import>
152 </macros> 232 </macros>
153 <expand macro="qiime_citation"/> 233 <expand macro="qiime_citation"/>
154 </tool> 234 </tool>