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comparison IDchoice/IDchoice.xml @ 0:b7a6a88f518a draft

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author melpetera
date Thu, 11 Oct 2018 05:47:29 -0400
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1 <tool id="idchoice" name="ID choice" version="18.01">
2 <description>Choosing a particular column in your metadata to be considered as Identifiers</description>
3 <requirements>
4 <requirement type="package" version="1.1_4">r-batch</requirement>
5 </requirements>
6 <command interpreter="Rscript">
7 IDchoice_wrap.R
8 dataMatrix_in "$dataMatrix_in"
9 Metadata_in "$Metadata_in"
10
11 metatype "$metatype"
12 col_name "$col_name"
13 makeunique "$makeunique"
14
15 DM_out "$DM_out"
16 meta_out "$meta_out"
17
18 </command>
19
20 <inputs>
21
22 <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
23 <param name="Metadata_in" type="data" label="Metadata file containing your new IDs" help="Sample metadata or variable metadata" format="tabular" />
24
25 <param name="metatype" label="Which ID do you want to change?" type="select" display="radio" help="">
26 <option value="sample">Samples</option>
27 <option value="variable" selected="True">Variables</option>
28 </param>
29
30 <param name="col_name" label="Name of the column to consider as new ID" type="text" value="" help="Exact name; must be in your metadata file" />
31
32 <param name="makeunique" label="Force unicity if not unique?" type="select" display="radio" help="">
33 <option value="yes">Yes</option>
34 <option value="no" selected="True">No</option>
35 </param>
36
37 </inputs>
38
39 <outputs>
40 <data name="DM_out" label="ID_${dataMatrix_in.name}" format="tabular" ></data>
41 <data name="meta_out" label="ID_${Metadata_in.name}" format="tabular" ></data>
42 </outputs>
43
44
45 <tests>
46 <test>
47 <param name="dataMatrix_in" value="input_IDc_dataMatrix.txt"/>
48 <param name="Metadata_in" value="input_IDc_variableMetadata.txt"/>
49 <param name="metatype" value="variable"/>
50 <param name="col_name" value="B"/>
51 <param name="makeunique" value="yes"/>
52 <output name="DM_out" file="output1_IDc_dataMatrix.tabular"/>
53 <output name="meta_out" file="output1_IDc_variableMetadata.tabular"/>
54 </test>
55 <test>
56 <param name="dataMatrix_in" value="input_IDc_dataMatrix.txt"/>
57 <param name="Metadata_in" value="input_IDc_sampleMetadata.txt"/>
58 <param name="metatype" value="sample"/>
59 <param name="col_name" value="AAA"/>
60 <param name="makeunique" value="yes"/>
61 <output name="DM_out" file="output2_IDc_dataMatrix.tabular"/>
62 <output name="meta_out" file="output2_IDc_sampleMetadata.tabular"/>
63 </test>
64 </tests>
65
66
67 <help>
68
69 .. class:: infomark
70
71 **Authors**
72 | Melanie Petera - PFEM ; INRA ; MetaboHUB
73
74 ---------------------------------------------------
75
76 ========================
77 ID Choice
78 ========================
79
80 -----------
81 Description
82 -----------
83
84 Change the current identifiers into new ones defined in your metadata file.
85 Can be used for sample ID as well as variable ID.
86
87
88
89 -----------
90 Input files
91 -----------
92
93 +----------------------------+---------+
94 | Parameter : num + label | Format |
95 +============================+=========+
96 | 1 : Data matrix file | tabular |
97 +----------------------------+---------+
98 | 2 : Metadata file | tabular |
99 +----------------------------+---------+
100
101
102 Data matrix file contains the intensity values of the variables.
103 |
104
105 Metadata file is meant to be chosen from sample metadata and variable metadata files.
106 | It should include a column containing your wanted IDs.
107 |
108
109 ----------
110 Parameter
111 ----------
112
113 Which ID do you want to change?
114 | This must be consistant with the metadata file you chose as input
115 |
116
117 Name of the column to consider as new ID
118 | Must be one of your metadata file's column
119 |
120
121 Force unicity if not unique?
122 | If no (default value), if your ID column does not contain unique values, it will stop the process and send you back an explicit error.
123 | If yes, non-unique values will be converted by adding "_x" at the end of concerned IDs.
124 |
125
126
127 ------------
128 Output file
129 ------------
130
131 ID_metadata
132 | tabular output
133 | Corresponds to the input metadata file with new IDs as first column
134 |
135
136 ID_datamatrix
137 | tabular output
138 | Corresponds to the input data matrix file with new IDs
139 |
140
141
142 ---------------------------------------------------
143
144 ----------------------
145 Additional information
146 ----------------------
147
148
149 .. class:: warningmark
150
151 For more information about input files, refer to the corresponding "W4M HowTo" page:
152 | `W4M table format for Galaxy &lt;http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf&gt;`_
153 |
154
155
156
157
158 </help>
159 </tool>