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comparison center_scale.xml @ 0:bcbd7179d8ec draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
author artbio
date Thu, 11 Jul 2019 13:31:20 -0400
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1 <tool id="center_scale" name="Center or scale (standardize) data" version="0.9.0">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="1.6.0">r-optparse</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" level="fatal" description="Tool exception" />
8 </stdio>
9 <command detect_errors="exit_code"><![CDATA[
10 Rscript $__tool_directory__/center_scale.R
11 --data '$input'
12 --center '$center'
13 --scale '$scale'
14 #if $factor.factor_options == 'TRUE':
15 --factor '$file'
16 #end if
17 --output '$output'
18 ]]></command>
19 <inputs>
20 <param name="input" type="data" format="tabular" label="Input file with values to transform"
21 help="Must be tabular separated with columns and row names, variables in rows, observations in columns" />
22 <param name="center" type="select" label="Center data to mean">
23 <option value="TRUE" selected="true">Yes</option>
24 <option value="FALSE">No</option>
25 </param>
26 <param name="scale" type="select" label="Scale data to standard deviation">
27 <option value="TRUE" selected="true">Yes</option>
28 <option value="FALSE">No</option>
29 </param>
30 <conditional name="factor">
31 <param name="factor_options" type="select" label="group data by factor ?">
32 <option value="TRUE">Yes</option>
33 <option value="FALSE" selected="true">No</option>
34 </param>
35 <when value="TRUE">
36 <param name="file" type="data" format="tabular" label="Grouping map"
37 help="A two-column observation|factor_level table that assigns group ids to observations" />
38 </when>
39 <when value="FALSE">
40 </when>
41 </conditional>
42 </inputs>
43 <outputs>
44 <data name="output" format="tabular" label="scale ${on_string}" />
45 </outputs>
46 <tests>
47 <test>
48 <param name="input" value="mini.data.counts.tsv" ftype="tabular"/>
49 <output name="output" file="full_standardize.tab" ftype="tabular"/>
50 </test>
51 <test>
52 <param name="input" value="mini.data.counts.tsv" ftype="tabular"/>
53 <param name="scale" value="FALSE"/>
54 <output name="output" file="full_center.tab" ftype="tabular"/>
55 </test>
56 <test>
57 <param name="input" value="mini.data.counts.tsv" ftype="tabular" />
58 <param name="factor_options" value="TRUE" />
59 <param name="file" value="mini.data.factor.tsv" ftype="tabular" />
60 <output name="output" file="group_standardize.tab" ftype="tabular"/>
61 </test>
62 <test>
63 <param name="input" value="mini.data.counts.tsv" ftype="tabular" />
64 <param name="scale" value="FALSE"/>
65 <param name="factor_options" value="TRUE" />
66 <param name="file" value="mini.data.factor.tsv" ftype="tabular" />
67 <output name="output" file="group_center.tab" ftype="tabular"/>
68 </test>
69 </tests>
70 <help>
71
72 **What it does**
73
74 The tool perform various normalization operations on a data table, including mean centering,
75 standard deviation rescaling, or both (standardization).
76
77 In addition, these operations can be performed on subsets of observations, is the user provides
78 a two-column table that maps observations to groups (factor levels).
79
80 **Inputs**
81
82 A data table with observations (samples, library sequencings) in columns (library names
83 are column names) and variables (genes) in rows (gene names are row names).
84
85 Optionally, a two-column table may be used to map observations to a factor level. In this
86 case, normalization operations will be performed by group having same level.
87
88 **Outputs**
89
90 A table with same numbers of columns and rows as input table, and transformed values.
91
92 </help>
93 <citations>
94 <citation type="bibtex">
95 @Manual{,
96 title = {R: A Language and Environment for Statistical Computing},
97 author = {{R Core Team}},
98 organization = {R Foundation for Statistical Computing},
99 address = {Vienna, Austria},
100 year = {2014},
101 url = {http://www.R-project.org/},
102 }
103 </citation>
104 </citations>
105 </tool>