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comparison TableMerge/tablemerge.xml @ 0:902ab790fb7b draft

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author melpetera
date Thu, 23 Feb 2017 04:37:49 -0500
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1 <tool id="tablemerge" name="Table Merge" version="1.0.1">
2 <description>Merging dataMatrix with a metadata table</description>
3 <requirements>
4 <requirement type="package" version="1.1_4">r-batch</requirement>
5 </requirements>
6 <command interpreter="Rscript">
7 tablemerge_wrap.R
8 dataMatrix_in "$dataMatrix_in"
9 Metadata_in "$Metadata_in"
10
11 metatype "$metatype"
12
13 combined_out "$combined_out"
14
15 </command>
16
17 <inputs>
18 <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
19 <param name="Metadata_in" type="data" label="Metadata file" help="Sample metadata or variable metadata" format="tabular" />
20
21 <param name="metatype" label="Type of metadata" type="select" display="radio" help="">
22 <option value="sample">Sample metadata</option>
23 <option value="variable">Variable metadata</option>
24 </param>
25
26 </inputs>
27
28 <outputs>
29 <data name="combined_out" label="Combined_${Metadata_in.name}" format="tabular" ></data>
30 </outputs>
31
32 <tests>
33 <test>
34 <param name="dataMatrix_in" value="input_TM12_dataMatrix.txt"/>
35 <param name="Metadata_in" value="input_TM1_variableMetadata.txt"/>
36 <param name="metatype" value="variable"/>
37 <output name="combined_out" file="output_TM1_expected.tabular"/>
38 </test>
39 <test>
40 <param name="dataMatrix_in" value="input_TM12_dataMatrix.txt"/>
41 <param name="Metadata_in" value="input_TM2_sampleMetadata.txt"/>
42 <param name="metatype" value="sample"/>
43 <output name="combined_out" file="output_TM2_expected.tabular"/>
44 </test>
45 </tests>
46
47
48 <help>
49
50 .. class:: infomark
51
52 **Authors**
53 | Melanie Petera - PFEM ; INRA ; MetaboHUB
54
55 ---------------------------------------------------
56
57 ========================
58 Table Merge
59 ========================
60
61 -----------
62 Description
63 -----------
64
65 Merges the data matrix with a selected metadata file (sample metadata or variable metadata)
66 to obtain a single file.
67
68
69
70 -----------
71 Input files
72 -----------
73
74 +----------------------------+---------+
75 | Parameter : num + label | Format |
76 +============================+=========+
77 | 1 : Data matrix file | tabular |
78 +----------------------------+---------+
79 | 2 : Metadata file | tabular |
80 +----------------------------+---------+
81
82
83 Data matrix file contains the intensity values of the variables.
84 |
85
86 Metadata file is meant to be chosen from sample metadata and variable metadata files.
87 |
88
89 ----------
90 Parameter
91 ----------
92
93 Type of metadata
94 | Specify which type of metadata table is given as Metadata file
95 |
96
97
98 ------------
99 Output file
100 ------------
101
102
103 Combined_Metadata
104 | tabular output
105 | Corresponds to the input metadata file completed as new columns by the intensities in the input data matrix file
106 |
107
108
109 ---------------------------------------------------
110
111 ---------------
112 Working example
113 ---------------
114
115
116 .. class:: warningmark
117
118 For more information about input files, refer to the corresponding "W4M HowTo" page:
119 | `W4M table format for Galaxy &lt;http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf&gt;`_
120 |
121
122
123
124
125 </help>
126 </tool>