Mercurial > repos > melpetera > intensity_checks

comparison Intchecks/xml_intensity_check.xml @ 0:c2c2e1be904a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author melpetera
date Thu, 11 Oct 2018 05:33:19 -0400
parents
children 4973a2104cfd
comparison
equal deleted inserted replaced
-1:000000000000 0:c2c2e1be904a
1 <tool id="intens_check" name="Intensity Check" version="1.0.1">
2 <description>Adding informations about intensities in the Variable metadata</description>
3 <requirements>
4 <requirement type="package" version="1.1_4">r-batch</requirement>
5 </requirements>
6 <command interpreter="Rscript">
7
8 wrapper_intensity_check.R
9
10 dataMatrix_in "$dataMatrix_in"
11 sampleMetadata_in "$sampleMetadata_in"
12 variableMetadata_in "$variableMetadata_in"
13
14 class_col "$class_col"
15
16 type "${type_cond.type}"
17 #if $type_cond.type == "One_class" :
18 class1 "${type_cond.class1}"
19 #end if
20
21 variableMetadata_out "$variableMetadata_out"
22 graphs_out "$graphs_out"
23 </command>
24
25 <inputs>
26 <param name="dataMatrix_in" type="data" label="Data Matrix file" help="" format="tabular" />
27 <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
28 <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
29
30 <param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" label="Class column" help="Class column in Sample metadata" />
31
32 <conditional name="type_cond">
33 <param name="type" type="select" label="Type" display="radio" help="Which class do you want to test ?">
34 <option value="One_class">Tests between one class and the remaining samples </option>
35 <option value="Each_class">Tests for each class </option>
36 </param>
37 <when value="One_class">
38 <param name="class1" type="text" label="Selected class" help="This class is the numerator for the fold test" />
39 </when>
40 <when value="Each_class">
41 </when>
42 </conditional>
43
44 </inputs>
45
46 <outputs>
47 <data name="variableMetadata_out" label="IC_${variableMetadata_in.name}" format="tabular" />
48 <data name="graphs_out" label="IC_Graphs" format="pdf" />
49 </outputs>
50
51 <help>
52
53 .. class:: infomark
54
55 **Authors**
56 | Anthony Fernandes - PFEM ; INRA
57
58 ---------------------------------------------------
59
60 ========================
61 Intensity Check
62 ========================
63
64 -----------
65 Description
66 -----------
67
68 This tool performs two tests: the fold calculation, the number and the proportion of missing values.
69
70 **Fold:**
71 The test calculates the ratio between two classes.
72 In the column name, the first class specified is the one used like numerator for the ratio.
73
74 **Missing values:**
75 This tool calculates the number and the proportion of missing values considering the class.
76 Missing values in numerical columns of data must be coded NA.
77
78 **Two types of tests:**
79 | - Between **one class** and the remaining samples: if you have only two classes or if you want to test only one class.
80 | - **Each class**: if the column class contains at least three classes and you want to test each of them.
81
82 -----------
83 Input files
84 -----------
85
86 +----------------------------+------------+
87 | Parameter | Format |
88 +============================+============+
89 | 1 : Data Matrix file | tabular |
90 +----------------------------+------------+
91 | 2 : Sample metadata file | tabular |
92 +----------------------------+------------+
93 | 3 : Variable metadata file | tabular |
94 +----------------------------+------------+
95
96 ----------
97 Parameters
98 ----------
99
100 **Class column**
101 | Select the class column in Sample metadata.
102
103 **Type**
104 | Two options:
105 | - "One class" allows to perform tests on one class against the remaining samples.
106 | - "Each class" allows to add several columns with the ratio and the number of missing values for each class.
107
108 **Selected class**
109 | If the type is "one class", specify it to calculate the ratio and the number of missing values.
110
111 ------------
112 Output file
113 ------------
114
115 **Variable metadata file**
116 | Contains the previous columns in variable metadata and the new ones with fold tests, numbers and proportion of missing values.
117
118 **Graphs file**
119 | Contains barplots with the proportion of NA considering classes and boxplots with the folds values
120
121 </help>
122
123
124 </tool>
125