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comparison qiime2/qiime_longitudinal_pairwise-distances.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_pairwise-distances" name="qiime longitudinal pairwise-distances" version="2018.4">
3 <description> - Paired pairwise distance testing and boxplots</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime longitudinal pairwise-distances --p-state-column="$pstatecolumn"
10
11 #def list_dict_to_string(list_dict):
12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
13 #for d in list_dict[1:]:
14 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
15 #end for
16 #return $file_list
17 #end def
18
19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-group-column="$pgroupcolumn" --p-state-2="$pstate2" --p-individual-id-column="$pindividualidcolumn" --p-state-1="$pstate1" --i-distance-matrix=$idistancematrix
20 #if str($preplicatehandling) != 'None':
21 --p-replicate-handling=$preplicatehandling
22 #end if
23
24 #if str($cmdconfig) != 'None':
25 --cmd-config=$cmdconfig
26 #end if
27 --o-visualization=ovisualization
28
29 #if $pparametric:
30 --p-parametric
31 #else
32 --p-no-parametric
33 #end if
34
35 #if str($ppalette) != 'None':
36 --p-palette=$ppalette
37 #end if
38 ;
39 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
40 && cp -r out/* '$ovisualization.files_path'
41 && mv '$ovisualization.files_path/index.html' '$ovisualization'
42 ]]>
43 </command>
44 <inputs>
45 <param format="qza,no_unzip.zip" label="--i-distance-matrix: DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
46
47 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
48 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
49 </repeat>
50
51 <param label="--p-group-column: Metadata column on which to separate groups for comparison [required]" name="pgroupcolumn" optional="False" type="text"/>
52 <param label="--p-state-column: Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text"/>
53
54 <param label="--p-state-1: Baseline state column value. [required]" name="pstate1" optional="False" type="text"/>
55 <param label="--p-state-2: State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text"/>
56
57 <param label="--p-individual-id-column: 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"/>
58 <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" checked="False" type="boolean"/>
59
60 <param label="--p-palette: Color palette to use for generating
61 boxplots. [default: Set1]" name="ppalette" optional="True" type="select">
62 <option selected="True" value="None">Selection is Optional</option>
63 <option value="Accent">Accent</option>
64 <option value="tab20">tab20</option>
65 <option value="Pastel2">Pastel2</option>
66 <option value="plasma">plasma</option>
67 <option value="viridis">viridis</option>
68 <option value="rainbow">rainbow</option>
69 <option value="Pastel1">Pastel1</option>
70 <option value="inferno">inferno</option>
71 <option value="magma">magma</option>
72 <option value="tab20b">tab20b</option>
73 <option value="Set3">Set3</option>
74 <option value="Set2">Set2</option>
75 <option value="Dark2">Dark2</option>
76 <option value="Set1">Set1</option>
77 <option value="tab10">tab10</option>
78 <option value="tab20c">tab20c</option>
79 <option value="terrain">terrain</option>
80 <option value="Paired">Paired</option>
81 </param>
82
83 <param label="--p-replicate-handling: Choose how replicate samples are handled. If
84 replicates are detected, 'error' causes
85 method to fail; 'drop' will discard all
86 replicated samples; 'random' chooses one
87 representative at random from among
88 replicates. [default: error]" name="preplicatehandling" optional="True" type="select">
89 <option selected="True" value="None">Selection is Optional</option>
90 <option value="error">error</option>
91 <option value="random">random</option>
92 <option value="drop">drop</option>
93 </param>
94
95 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
96 </inputs>
97 <outputs>
98 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
99 </outputs>
100 <help>
101 <![CDATA[
102 Paired pairwise distance testing and boxplots
103 ----------------------------------------------
104
105 Performs pairwise distance testing between sample pairs from each subject.
106 Sample pairs may represent a typical intervention study, e.g., samples
107 collected pre- and post-treatment; paired samples from two different
108 timepoints (e.g., in a longitudinal study design), or identical samples
109 receiving different two different treatments. This action tests whether the
110 pairwise distance between each subject pair differs between groups (e.g.,
111 groups of subjects receiving different treatments) and produces boxplots of
112 paired distance distributions for each group.
113
114 Parameters
115 ----------
116 distance_matrix : DistanceMatrix
117 Matrix of distances between pairs of samples.
118 metadata : Metadata
119 Sample metadata file containing individual_id_column.
120 group_column : Str
121 Metadata column on which to separate groups for comparison
122 state_column : Str
123 Metadata column containing state (e.g., Time) across which samples are
124 paired.
125 state_1 : Str
126 Baseline state column value.
127 state_2 : Str
128 State column value to pair with baseline.
129 individual_id_column : Str
130 Metadata column containing subject IDs to use for pairing samples.
131 WARNING: if replicates exist for an individual ID at either state_1 or
132 state_2, that subject will be dropped and reported in standard output
133 by default. Set replicate_handling="random" to instead randomly select
134 one member.
135 parametric : Bool, optional
136 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
137 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
138 palette : Str % Choices({'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'inferno', 'magma', 'plasma', 'rainbow', 'tab10', 'tab20', 'tab20b', 'tab20c', 'terrain', 'viridis'}), optional
139 Color palette to use for generating boxplots.
140 replicate_handling : Str % Choices({'drop', 'error', 'random'}), optional
141 Choose how replicate samples are handled. If replicates are detected,
142 "error" causes method to fail; "drop" will discard all replicated
143 samples; "random" chooses one representative at random from among
144 replicates.
145
146 Returns
147 -------
148 visualization : Visualization
149 \
150 ]]>
151 </help>
152 <macros>
153 <import>qiime_citation.xml</import>
154 </macros>
155 <expand macro="qiime_citation" />
156 </tool>