annotate w4mclassfilter.xml @ 0:bab3a658f74e draft

planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
author eschen42
date Tue, 09 May 2017 18:34:35 -0400
parents
children 23c6d271def9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
1 <tool id="W4MClassFilter" name="W4MClassFilter" version="0.98.1">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
2 <description>Filter W4M data by sample class</description>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
3
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
4 <requirements>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
5 <requirement type="package" version="3.3.1">r-base</requirement>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
6 <requirement type="package" version="1.1_4">r-batch</requirement>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
7 <requirement type="package" version="0.98.1">w4mclassfilter</requirement>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
8 </requirements>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
9
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
10 <stdio>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
11 <exit_code range="1:" level="fatal" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
12 </stdio>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
13
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
14
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
15 <command detect_errors="aggressive"><![CDATA[
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
16 Rscript $__tool_directory__/w4mclassfilter_wrapper.R
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
17 dataMatrix_in "$dataMatrix_in"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
18 sampleMetadata_in "$sampleMetadata_in"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
19 variableMetadata_in "$variableMetadata_in"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
20 sampleclassNames "$sampleclassNames"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
21 inclusive "$inclusive"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
22 classnameColumn "$classnameColumn"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
23 samplenameColumn "$samplenameColumn"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
24 dataMatrix_out "$dataMatrix_out"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
25 sampleMetadata_out "$sampleMetadata_out"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
26 variableMetadata_out "$variableMetadata_out"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
27 information "$information"
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
28 ]]></command>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
29
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
30 <inputs>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
31 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
32 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
33 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
34 <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names of sample classes to filter in or out; defaults to no names" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
35 <param name="inclusive" label="Include named classes" type="select" help="filter-in - include only the named sample classes; filter-out (the default) - exclude only the named sample classes">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
36 <option value="TRUE">filter-in</option>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
37 <option value="FALSE" selected="true">filter-out</option>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
38 </param>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
39 <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" help="name of the column in sample metadata that has the values to be tested against the 'classes' input parameter - defaults to 'class'" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
40 <param name="samplenameColumn" label="Column that names the sample" type="text" value = "sampleMetadata" help="name of the column in sample metadata that has the name of the sample - defaults to 'sampleMetadata'" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
41 </inputs>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
42 <outputs>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
43 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
44 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
45 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
46 <data name="information" label="${tool.name}__information.txt" format="txt"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
47 </outputs>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
48
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
49 <tests>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
50 <test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
51 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
52 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
53 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
54 <param name="classnameColumn" value="gender"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
55 <param name="sampleclassNames" value="M"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
56 <param name="samplenameColumn" value="sampleMetadata"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
57 <param name="inclusive" value="filter-in"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
58 <param name="information" value="test-information.txt"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
59 <output name="dataMatrix_out">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
60 <assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
61 <not_has_text text="HU_028" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
62 <not_has_text text="HU_051" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
63 <not_has_text text="HU_060" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
64 <not_has_text text="HU_110" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
65 <not_has_text text="HU_149" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
66 <not_has_text text="HU_152" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
67 <not_has_text text="HU_175" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
68 <not_has_text text="HU_178" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
69 <not_has_text text="HU_185" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
70 <not_has_text text="HU_204" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
71 <not_has_text text="HU_208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
72 <has_text text="HU_017" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
73 <has_text text="HU_034" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
74 <has_text text="HU_078" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
75 <has_text text="HU_091" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
76 <has_text text="HU_093" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
77 <has_text text="HU_099" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
78 <has_text text="HU_130" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
79 <has_text text="HU_134" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
80 <has_text text="HU_138" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
81 <has_text text="HMDB03193" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
82 <not_has_text text="HMDB00822" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
83 <has_text text="HMDB01101" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
84 <has_text text="HMDB01101.1" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
85 <has_text text="HMDB10348" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
86 <has_text text="HMDB59717" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
87 <has_text text="HMDB13189" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
88 <has_text text="HMDB00299" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
89 <has_text text="HMDB00191" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
90 <has_text text="HMDB00518" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
91 <has_text text="HMDB00715" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
92 <has_text text="HMDB01032" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
93 <has_text text="HMDB00208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
94 <has_text text="HMDB04824" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
95 <has_text text="HMDB00512" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
96 <has_text text="HMDB00251" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
97 </assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
98 </output>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
99 </test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
100 <test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
101 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
102 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
103 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
104 <param name="classnameColumn" value="gender"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
105 <param name="sampleclassNames" value="M"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
106 <param name="samplenameColumn" value="sampleMetadata"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
107 <param name="inclusive" value="filter-in"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
108 <param name="information" value="test-information.txt"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
109 <output name="sampleMetadata_out">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
110 <assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
111 <not_has_text text="HU_028" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
112 <not_has_text text="HU_051" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
113 <not_has_text text="HU_060" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
114 <not_has_text text="HU_110" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
115 <not_has_text text="HU_149" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
116 <not_has_text text="HU_152" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
117 <not_has_text text="HU_175" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
118 <not_has_text text="HU_178" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
119 <not_has_text text="HU_185" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
120 <not_has_text text="HU_204" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
121 <not_has_text text="HU_208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
122 <has_text text="HU_017" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
123 <has_text text="HU_034" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
124 <has_text text="HU_078" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
125 <has_text text="HU_091" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
126 <has_text text="HU_093" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
127 <has_text text="HU_099" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
128 <has_text text="HU_130" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
129 <has_text text="HU_134" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
130 <has_text text="HU_138" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
131 </assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
132 </output>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
133 </test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
134 <test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
135 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
136 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
137 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
138 <param name="classnameColumn" value="gender"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
139 <param name="sampleclassNames" value="M"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
140 <param name="samplenameColumn" value="sampleMetadata"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
141 <param name="inclusive" value="filter-in"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
142 <param name="information" value="test-information.txt"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
143 <output name="variableMetadata_out">
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
144 <assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
145 <has_text text="HMDB03193" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
146 <not_has_text text="HMDB00822" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
147 <has_text text="HMDB01101" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
148 <has_text text="HMDB01101.1" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
149 <has_text text="HMDB10348" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
150 <has_text text="HMDB59717" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
151 <has_text text="HMDB13189" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
152 <has_text text="HMDB00299" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
153 <has_text text="HMDB00191" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
154 <has_text text="HMDB00518" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
155 <has_text text="HMDB00715" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
156 <has_text text="HMDB01032" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
157 <has_text text="HMDB00208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
158 <has_text text="HMDB04824" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
159 <has_text text="HMDB00512" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
160 <has_text text="HMDB00251" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
161 </assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
162 </output>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
163 </test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
164 </tests>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
165
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
166
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
167
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
168 <help>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
169
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
170 .. class:: infomark
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
171
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
172 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
173
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
174 --------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
175
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
176 .. class:: infomark
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
177
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
178 **R package**
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
179
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
180 The *w4mclassfilter* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases).
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
181
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
182 -----------------------------------------------------------------------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
183
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
184 .. class:: infomark
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
185
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
186 **Tool updates**
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
187
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
188 See the **NEWS** section at the bottom of this page
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
189
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
190 ---------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
191
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
192 ==============================================
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
193 Filter Workflow4Metabolomics data matrix files
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
194 ==============================================
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
195
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
196 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
197 Description
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
198 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
199
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
200 Filter set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample class
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
201
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
202 --------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
203 Comments
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
204 --------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
205
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
206 The *inclusive* parameter indicates:
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
207 - when 'filter-in', that only the sample-classes named should be included
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
208 - when 'filter-out', that all sample-classes should be included excepting the sample-classes named
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
209
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
210 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
211 Input files
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
212 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
213
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
214 +---------------------------+------------+
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
215 | File | Format |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
216 +===========================+============+
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
217 | 1) Data matrix | tabular |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
218 +---------------------------+------------+
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
219 | 2) Sample metadata | tabular |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
220 +---------------------------+------------+
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
221 | 3) Variable metadata | tabular |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
222 +---------------------------+------------+
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
223
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
224
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
225 ----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
226 Parameters
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
227 ----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
228
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
229 Data matrix file
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
230 | variable x sample **dataMatrix** tabular separated file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
231 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
232
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
233 Sample metadata file
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
234 | sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
235 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
236
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
237 Variable metadata file
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
238 | variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
239 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
240
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
241 Names of sample classes (default = no names)
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
242 | comma-separated names of sample classes to include or exclude
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
243 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
244
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
245 Include named classes (default = filter-out)
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
246 | *filter-in* - include only the named sample classes
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
247 | *filter-out* - exclude only the named sample classes
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
248 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
249
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
250 Column that names the sample-class (default = 'class')
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
251 | name of the column in sample metadata that has the values to be tested against the 'classes' input parameter
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
252 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
253
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
254 Column that names the sample (default = 'sampleMetadata')
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
255 | name of the column in sample metadata that has the name of the sample
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
256 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
257
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
258
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
259 ------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
260 Output files
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
261 ------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
262
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
263
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
264 sampleMetadata_out.tabular
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
265 | **sampleMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for samples that have been filtered out
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
266 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
267
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
268 variableMetadata_out.tabular
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
269 | **variableMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance)
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
270 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
271
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
272 dataMatrix_out.tabular
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
273 | **dataMatrix** tabular separated file identical to the file given as argument, excepting lacking columns for samples that have been filtered out (because of the sample-classes specified in the input parameters) and rows for variables (xC-MS features) that have been filtered out (because of zero variance)
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
274 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
275
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
276 information.txt
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
277 | Text file with all messages and warnings generated during the computation
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
278 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
279
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
280 -----------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
281
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
282 ----
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
283 NEWS
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
284 ----
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
285
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
286 CHANGES IN VERSION 0.98.1
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
287 =========================
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
288
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
289 NEW FEATURES
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
290
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
291 First release - R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample.
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
292
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
293 *dataMatrix* *is* modified by the tool, so it *does* appear as an output file
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
294
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
295 INTERNAL MODIFICATIONS
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
296
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
297 none
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
298
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
299 </help>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
300 <citations>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
301 </citations>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
302 </tool>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
303 <!-- vim: et sw=2 ts=2 :
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
304 -->