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comparison qiime2/qiime_longitudinal_pairwise-differences.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-differences" name="qiime longitudinal pairwise-differences" version="2019.7"> 2 <tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences"
3 <description> - Paired difference testing and boxplots</description> 3 version="2020.8">
4 <requirements> 4 <description>Paired difference 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-differences 9 qiime longitudinal pairwise-differences
9 10
10 --p-metric="$pmetric" 11 #if str($itable) != 'None':
11 --p-state-column="$pstatecolumn" 12 --i-table=$itable
12 --p-state-1="$pstate1" 13 #end if
13 --p-state-2="$pstate2" 14 # if $input_files_mmetadatafile:
14 15 # def list_dict_to_string(list_dict):
15 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 = $pindividualidcolumn_temp
66 #end if
16 #if '__sq__' in str($pindividualidcolumn): 67 #if '__sq__' in str($pindividualidcolumn):
17 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'") 68 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
18 #set $pindividualidcolumn = $pindividualidcolumn_temp 69 #set $pindividualidcolumn = $pindividualidcolumn_temp
19 #end if 70 #end if
20 #if str($pindividualidcolumn): 71 #if '__db__' in str($pindividualidcolumn):
21 --p-individual-id-column="$pindividualidcolumn" 72 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
22 #end if 73 #set $pindividualidcolumn = $pindividualidcolumn_temp
23 74 #end if
24 75
25 76 --p-individual-id-column=$pindividualidcolumn
26 #if str($itable) != 'None': 77
27 --i-table=$itable 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 = $pgroupcolumn_temp
28 #end if 98 #end if
29 99
30 #if str($pgroupcolumn): 100 #if str($pgroupcolumn):
31 --p-group-column="$pgroupcolumn" 101 --p-group-column=$pgroupcolumn
32 #end if 102 #end if
33 103
34 #if $pparametric: 104 #if $pparametric:
35 --p-parametric 105 --p-parametric
36 #end if 106 #end if
37 107
38 #if str($ppalette) != 'None': 108 #if str($ppalette) != 'None':
39 --p-palette=$ppalette 109 --p-palette=$ppalette
40 #end if 110 #end if
41 111
42 #if str($preplicatehandling) != 'None': 112 #if str($preplicatehandling) != 'None':
43 --p-replicate-handling=$preplicatehandling 113 --p-replicate-handling=$preplicatehandling
44 #end if 114 #end if
45
46
47 #if $input_files_mmetadatafile:
48 #def list_dict_to_string(list_dict):
49 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
50 #for d in list_dict[1:]:
51 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
52 #end for
53 #return $file_list
54 #end def
55 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
56 #end if
57
58 115
59 --o-visualization=ovisualization 116 --o-visualization=ovisualization
117
118 #if str($examples) != 'None':
119 --examples=$examples
120 #end if
121
60 ; 122 ;
61 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 123 cp odistancematrix.qza $odistancematrix
124
125 ;
126 qiime tools export ovisualization.qzv --output-path out
127 && mkdir -p '$ovisualization.files_path'
62 && cp -r out/* '$ovisualization.files_path' 128 && cp -r out/* '$ovisualization.files_path'
63 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 129 && mv '$ovisualization.files_path/index.html' '$ovisualization'
64 ]]></command> 130
65 <inputs> 131 ]]></command>
66 <param label="--p-metric: TEXT Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text"/> 132 <inputs>
67 <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"/> 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" />
68 <param label="--p-state-1: TEXT Baseline state column value. [required]" name="pstate1" optional="False" type="text"/> 134 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
69 <param label="--p-state-2: TEXT State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text"/> 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" />
70 <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"/> 136 </repeat>
71 <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"/> 137 <param label="--p-metric: TEXT Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text" />
72 <param label="--p-group-column: TEXT Metadata column on which to separate groups for comparison [optional]" name="pgroupcolumn" optional="True" 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" />
73 <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"/> 139 <param label="--p-state-1: TEXT Baseline state column value. [required]" name="pstate1" optional="False" type="text" />
74 <param label="--p-palette: " name="ppalette" optional="True" type="select"> 140 <param label="--p-state-2: TEXT State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text" />
75 <option selected="True" value="None">Selection is Optional</option> 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" />
76 <option value="Set1">Set1</option> 142 <param label="--p-group-column: TEXT Metadata column on which to separate groups for comparison [optional]" name="pgroupcolumn" optional="False" type="text" />
77 <option value="Set2">Set2</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" />
78 <option value="Set3">Set3</option> 144 <param label="--p-palette: " name="ppalette" optional="True" type="select">
79 <option value="Pastel1">Pastel1</option> 145 <option selected="True" value="None">Selection is Optional</option>
80 <option value="Pastel2">Pastel2</option> 146 <option value="Set1">Set1</option>
81 <option value="Paired">Paired</option> 147 <option value="Set2">Set2</option>
82 <option value="Accent">Accent</option> 148 <option value="Set3">Set3</option>
83 <option value="Dark2">Dark2</option> 149 <option value="Pastel1">Pastel1</option>
84 <option value="tab10">tab10</option> 150 <option value="Pastel2">Pastel2</option>
85 <option value="tab20">tab20</option> 151 <option value="Paired">Paired</option>
86 <option value="tab20b">tab20b</option> 152 <option value="Accent">Accent</option>
87 <option value="tab20c">tab20c</option> 153 <option value="Dark2">Dark2</option>
88 <option value="viridis">viridis</option> 154 <option value="tab10">tab10</option>
89 <option value="plasma">plasma</option> 155 <option value="tab20">tab20</option>
90 <option value="inferno">inferno</option> 156 <option value="tab20b">tab20b</option>
91 <option value="magma">magma</option> 157 <option value="tab20c">tab20c</option>
92 <option value="terrain">terrain</option> 158 <option value="viridis">viridis</option>
93 <option value="rainbow">rainbow</option> 159 <option value="plasma">plasma</option>
94 </param> 160 <option value="inferno">inferno</option>
95 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select"> 161 <option value="magma">magma</option>
96 <option selected="True" value="None">Selection is Optional</option> 162 <option value="terrain">terrain</option>
97 <option value="error">error</option> 163 <option value="rainbow">rainbow</option>
98 <option value="random">random</option> 164 <option value="cividis">cividis</option>
99 <option value="drop">drop</option> 165 </param>
100 </param> 166 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
101 167 <option selected="True" value="None">Selection is Optional</option>
102 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> 168 <option value="error">error</option>
103 <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" /> 169 <option value="random">random</option>
104 </repeat> 170 <option value="drop">drop</option>
105 171 </param>
106 </inputs> 172 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
107 <outputs> 173
108 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 174 </inputs>
109 </outputs> 175
110 <help><![CDATA[ 176 <outputs>
177 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
178
179 </outputs>
180
181 <help><![CDATA[
111 Paired difference testing and boxplots 182 Paired difference testing and boxplots
112 ###################################### 183 ###############################################################
113 184
114 Performs paired difference testing between samples from each subject. 185 Performs paired difference testing between samples from each subject.
115 Sample pairs may represent a typical intervention study, e.g., samples 186 Sample pairs may represent a typical intervention study (e.g., samples
116 collected pre- and post-treatment; paired samples from two different 187 collected pre- and post-treatment), paired samples from two different
117 timepoints (e.g., in a longitudinal study design), or identical samples 188 timepoints (e.g., in a longitudinal study design), or identical samples
118 receiving different two different treatments. This action tests whether the 189 receiving different treatments. This action tests whether the change in a
119 change in a numeric metadata value "metric" differs from zero and differs 190 numeric metadata value "metric" differs from zero and differs between
120 between groups (e.g., groups of subjects receiving different treatments), 191 groups (e.g., groups of subjects receiving different treatments), and
121 and produces boxplots of paired difference distributions for each group. A 192 produces boxplots of paired difference distributions for each group. Note
122 feature table artifact is required input, though whether "metric" is 193 that "metric" can be derived from a feature table or metadata.
123 derived from the feature table or metadata is optional.
124 194
125 Parameters 195 Parameters
126 ---------- 196 ----------
127 metadata : Metadata 197 metadata : Metadata
128 Sample metadata file containing individual_id_column. 198 Sample metadata file containing individual_id_column.
144 group_column : Str, optional 214 group_column : Str, optional
145 Metadata column on which to separate groups for comparison 215 Metadata column on which to separate groups for comparison
146 parametric : Bool, optional 216 parametric : Bool, optional
147 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal- 217 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
148 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests. 218 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
149 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional 219 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis'), optional
150 Color palette to use for generating boxplots. 220 Color palette to use for generating boxplots.
151 replicate_handling : Str % Choices('error', 'random', 'drop'), optional 221 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
152 Choose how replicate samples are handled. If replicates are detected, 222 Choose how replicate samples are handled. If replicates are detected,
153 "error" causes method to fail; "drop" will discard all replicated 223 "error" causes method to fail; "drop" will discard all replicated
154 samples; "random" chooses one representative at random from among 224 samples; "random" chooses one representative at random from among
157 Feature table to optionally use for paired comparisons. 227 Feature table to optionally use for paired comparisons.
158 228
159 Returns 229 Returns
160 ------- 230 -------
161 visualization : Visualization 231 visualization : Visualization
162 ]]></help> 232 ]]></help>
163 <macros> 233 <macros>
164 <import>qiime_citation.xml</import> 234 <import>qiime_citation.xml</import>
165 </macros> 235 </macros>
166 <expand macro="qiime_citation"/> 236 <expand macro="qiime_citation"/>
167 </tool> 237 </tool>