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comparison qiime2/qiime_longitudinal_pairwise-distances.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_pairwise-distances" name="qiime longitudinal pairwise-distances" version="2019.4">
3 <description> - Paired pairwise distance testing and boxplots</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime longitudinal pairwise-distances
9
10 --i-distance-matrix=$idistancematrix
11 --p-group-column="$pgroupcolumn"
12 --p-state-column="$pstatecolumn"
13 --p-state-1="$pstate1"
14 --p-state-2="$pstate2"
15 --p-individual-id-column="$pindividualidcolumn"
16
17 #if $pparametric:
18 --p-parametric
19 #end if
20
21 #if str($ppalette) != 'None':
22 --p-palette=$ppalette
23 #end if
24
25 #if str($preplicatehandling) != 'None':
26 --p-replicate-handling=$preplicatehandling
27 #end if
28
29
30 #if $input_files_mmetadatafile:
31 #def list_dict_to_string(list_dict):
32 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
33 #for d in list_dict[1:]:
34 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
35 #end for
36 #return $file_list
37 #end def
38 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
39 #end if
40
41
42 --o-visualization=ovisualization
43 ;
44 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
45 && cp -r out/* '$ovisualization.files_path'
46 && mv '$ovisualization.files_path/index.html' '$ovisualization';
47 ]]></command>
48 <inputs>
49 <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"/>
50 <param label="--p-group-column: TEXT Metadata column on which to separate groups for comparison [required]" name="pgroupcolumn" optional="False" type="text"/>
51 <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"/>
52 <param label="--p-state-1: TEXT Baseline state column value. [required]" name="pstate1" optional="False" type="text"/>
53 <param label="--p-state-2: TEXT State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text"/>
54 <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"/>
55 <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"/>
56 <param label="--p-palette: " name="ppalette" optional="True" type="select">
57 <option selected="True" value="None">Selection is Optional</option>
58 <option value="Set1">Set1</option>
59 <option value="Set2">Set2</option>
60 <option value="Set3">Set3</option>
61 <option value="Pastel1">Pastel1</option>
62 <option value="Pastel2">Pastel2</option>
63 <option value="Paired">Paired</option>
64 <option value="Accent">Accent</option>
65 <option value="Dark2">Dark2</option>
66 <option value="tab10">tab10</option>
67 <option value="tab20">tab20</option>
68 <option value="tab20b">tab20b</option>
69 <option value="tab20c">tab20c</option>
70 <option value="viridis">viridis</option>
71 <option value="plasma">plasma</option>
72 <option value="inferno">inferno</option>
73 <option value="magma">magma</option>
74 <option value="terrain">terrain</option>
75 <option value="rainbow">rainbow</option>
76 </param>
77 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
78 <option selected="True" value="None">Selection is Optional</option>
79 <option value="error">error</option>
80 <option value="random">random</option>
81 <option value="drop">drop</option>
82 </param>
83
84 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
85 <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" />
86 </repeat>
87 </inputs>
88 <outputs>
89 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
90 </outputs>
91 <help><![CDATA[
92 Paired pairwise distance testing and boxplots
93 #############################################
94
95 Performs pairwise distance testing between sample pairs from each subject.
96 Sample pairs may represent a typical intervention study, e.g., samples
97 collected pre- and post-treatment; paired samples from two different
98 timepoints (e.g., in a longitudinal study design), or identical samples
99 receiving different two different treatments. This action tests whether the
100 pairwise distance between each subject pair differs between groups (e.g.,
101 groups of subjects receiving different treatments) and produces boxplots of
102 paired distance distributions for each group.
103
104 Parameters
105 ----------
106 distance_matrix : DistanceMatrix
107 Matrix of distances between pairs of samples.
108 metadata : Metadata
109 Sample metadata file containing individual_id_column.
110 group_column : Str
111 Metadata column on which to separate groups for comparison
112 state_column : Str
113 Metadata column containing state (e.g., Time) across which samples are
114 paired.
115 state_1 : Str
116 Baseline state column value.
117 state_2 : Str
118 State column value to pair with baseline.
119 individual_id_column : Str
120 Metadata column containing subject IDs to use for pairing samples.
121 WARNING: if replicates exist for an individual ID at either state_1 or
122 state_2, that subject will be dropped and reported in standard output
123 by default. Set replicate_handling="random" to instead randomly select
124 one member.
125 parametric : Bool, optional
126 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
127 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
128 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
129 Color palette to use for generating boxplots.
130 replicate_handling : Str % Choices('error', 'random', 'drop'), optional
131 Choose how replicate samples are handled. If replicates are detected,
132 "error" causes method to fail; "drop" will discard all replicated
133 samples; "random" chooses one representative at random from among
134 replicates.
135
136 Returns
137 -------
138 visualization : Visualization
139 ]]></help>
140 <macros>
141 <import>qiime_citation.xml</import>
142 </macros>
143 <expand macro="qiime_citation"/>
144 </tool>