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comparison qiime_longitudinal_pairwise-differences.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences" version="2018.4">
3 <description> - Paired difference 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-differences --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 + ' --m-metadata-file=' + 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-individual-id-column="$pindividualidcolumn" --p-state-1="$pstate1" --p-state-2="$pstate2" --p-metric="$pmetric"
20 #if str($itable) != 'None':
21 --i-table=$itable
22 #end if
23
24 #if str($cmdconfig) != 'None':
25 --cmd-config=$cmdconfig
26 #end if
27
28 #if str($preplicatehandling) != 'None':
29 --p-replicate-handling=$preplicatehandling
30 #end if
31
32 #if $pparametric:
33 --p-parametric
34 #else
35 --p-no-parametric
36 #end if
37
38 #if str($ppalette) != 'None':
39 --p-palette=$ppalette
40 #end if
41 --o-visualization=ovisualization;
42 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
43 && cp -r out/* '$ovisualization.files_path'
44 && mv '$ovisualization.files_path/index.html' '$ovisualization'
45 ]]>
46 </command>
47 <inputs>
48 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[RelativeFrequency] Feature table to optionally use for paired comparisons. [optional]" name="itable" optional="True" type="data"/>
49
50 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
51 <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" />
52 </repeat>
53
54 <param label="--p-group-column: Metadata column on which to separate groups for comparison [required]" name="pgroupcolumn" optional="False" type="text"/>
55 <param label="--p-metric: Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text"/>
56 <param label="--p-state-column: Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text"/>
57
58 <param label="--p-state-1: Baseline state column value. [required]" name="pstate1" optional="False" type="text"/>
59 <param label="--p-state-2: State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text"/>
60
61 <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"/>
62 <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"/>
63
64 <param label="--p-palette: Color palette to use for generating
65 boxplots. [default: Set1]" name="ppalette" optional="True" type="select">
66 <option selected="True" value="None">Selection is Optional</option>
67 <option value="Accent">Accent</option>
68 <option value="tab20">tab20</option>
69 <option value="Pastel2">Pastel2</option>
70 <option value="plasma">plasma</option>
71 <option value="viridis">viridis</option>
72 <option value="rainbow">rainbow</option>
73 <option value="Pastel1">Pastel1</option>
74 <option value="inferno">inferno</option>
75 <option value="magma">magma</option>
76 <option value="tab20b">tab20b</option>
77 <option value="Set3">Set3</option>
78 <option value="Set2">Set2</option>
79 <option value="Dark2">Dark2</option>
80 <option value="Set1">Set1</option>
81 <option value="tab10">tab10</option>
82 <option value="tab20c">tab20c</option>
83 <option value="terrain">terrain</option>
84 <option value="Paired">Paired</option>
85 </param>
86
87 <param label="--p-replicate-handling: Choose how replicate samples are handled. If
88 replicates are detected, 'error' causes
89 method to fail; 'drop' will discard all
90 replicated samples; 'random' chooses one
91 representative at random from among
92 replicates. [default: error]" name="preplicatehandling" optional="True" type="select">
93 <option selected="True" value="None">Selection is Optional</option>
94 <option value="error">error</option>
95 <option value="random">random</option>
96 <option value="drop">drop</option>
97 </param>
98
99 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
100 </inputs>
101 <outputs>
102 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
103 </outputs>
104 <help>
105 <![CDATA[
106 Paired difference testing and boxplots
107 ---------------------------------------
108
109 Performs paired difference testing between samples from each subject.
110 Sample pairs may represent a typical intervention study, e.g., samples
111 collected pre- and post-treatment; paired samples from two different
112 timepoints (e.g., in a longitudinal study design), or identical samples
113 receiving different two different treatments. This action tests whether the
114 change in a numeric metadata value "metric" differs from zero and differs
115 between groups (e.g., groups of subjects receiving different treatments),
116 and produces boxplots of paired difference distributions for each group. A
117 feature table artifact is required input, though whether "metric" is
118 derived from the feature table or metadata is optional.
119
120 Parameters
121 ----------
122 table : FeatureTable[RelativeFrequency], optional
123 Feature table to optionally use for paired comparisons.
124 metadata : Metadata
125 Sample metadata file containing individual_id_column.
126 group_column : Str
127 Metadata column on which to separate groups for comparison
128 metric : Str
129 Numerical metadata or artifact column to test.
130 state_column : Str
131 Metadata column containing state (e.g., Time) across which samples are
132 paired.
133 state_1 : Str
134 Baseline state column value.
135 state_2 : Str
136 State column value to pair with baseline.
137 individual_id_column : Str
138 Metadata column containing subject IDs to use for pairing samples.
139 WARNING: if replicates exist for an individual ID at either state_1 or
140 state_2, that subject will be dropped and reported in standard output
141 by default. Set replicate_handling="random" to instead randomly select
142 one member.
143 parametric : Bool, optional
144 Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
145 Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
146 palette : Str % Choices({'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'inferno', 'magma', 'plasma', 'rainbow', 'tab10', 'tab20', 'tab20b', 'tab20c', 'terrain', 'viridis'}), optional
147 Color palette to use for generating boxplots.
148 replicate_handling : Str % Choices({'drop', 'error', 'random'}), optional
149 Choose how replicate samples are handled. If replicates are detected,
150 "error" causes method to fail; "drop" will discard all replicated
151 samples; "random" chooses one representative at random from among
152 replicates.
153
154 Returns
155 -------
156 visualization : Visualization
157 \
158 ]]>
159 </help>
160 </tool>