Mercurial > repos > eschen42 > w4mclassfilter

comparison w4mclassfilter.xml @ 0:bab3a658f74e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
author eschen42
date Tue, 09 May 2017 18:34:35 -0400
parents
children 23c6d271def9
comparison
equal deleted inserted replaced
-1:000000000000 0:bab3a658f74e
1 <tool id="W4MClassFilter" name="W4MClassFilter" version="0.98.1">
2 <description>Filter W4M data by sample class</description>
3
4 <requirements>
5 <requirement type="package" version="3.3.1">r-base</requirement>
6 <requirement type="package" version="1.1_4">r-batch</requirement>
7 <requirement type="package" version="0.98.1">w4mclassfilter</requirement>
8 </requirements>
9
10 <stdio>
11 <exit_code range="1:" level="fatal" />
12 </stdio>
13
14
15 <command detect_errors="aggressive"><![CDATA[
16 Rscript $__tool_directory__/w4mclassfilter_wrapper.R
17 dataMatrix_in "$dataMatrix_in"
18 sampleMetadata_in "$sampleMetadata_in"
19 variableMetadata_in "$variableMetadata_in"
20 sampleclassNames "$sampleclassNames"
21 inclusive "$inclusive"
22 classnameColumn "$classnameColumn"
23 samplenameColumn "$samplenameColumn"
24 dataMatrix_out "$dataMatrix_out"
25 sampleMetadata_out "$sampleMetadata_out"
26 variableMetadata_out "$variableMetadata_out"
27 information "$information"
28 ]]></command>
29
30 <inputs>
31 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
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" />
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" />
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" />
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">
36 <option value="TRUE">filter-in</option>
37 <option value="FALSE" selected="true">filter-out</option>
38 </param>
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'" />
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'" />
41 </inputs>
42 <outputs>
43 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
44 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
45 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
46 <data name="information" label="${tool.name}__information.txt" format="txt"/>
47 </outputs>
48
49 <tests>
50 <test>
51 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
52 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
53 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
54 <param name="classnameColumn" value="gender"/>
55 <param name="sampleclassNames" value="M"/>
56 <param name="samplenameColumn" value="sampleMetadata"/>
57 <param name="inclusive" value="filter-in"/>
58 <param name="information" value="test-information.txt"/>
59 <output name="dataMatrix_out">
60 <assert_contents>
61 <not_has_text text="HU_028" />
62 <not_has_text text="HU_051" />
63 <not_has_text text="HU_060" />
64 <not_has_text text="HU_110" />
65 <not_has_text text="HU_149" />
66 <not_has_text text="HU_152" />
67 <not_has_text text="HU_175" />
68 <not_has_text text="HU_178" />
69 <not_has_text text="HU_185" />
70 <not_has_text text="HU_204" />
71 <not_has_text text="HU_208" />
72 <has_text text="HU_017" />
73 <has_text text="HU_034" />
74 <has_text text="HU_078" />
75 <has_text text="HU_091" />
76 <has_text text="HU_093" />
77 <has_text text="HU_099" />
78 <has_text text="HU_130" />
79 <has_text text="HU_134" />
80 <has_text text="HU_138" />
81 <has_text text="HMDB03193" />
82 <not_has_text text="HMDB00822" />
83 <has_text text="HMDB01101" />
84 <has_text text="HMDB01101.1" />
85 <has_text text="HMDB10348" />
86 <has_text text="HMDB59717" />
87 <has_text text="HMDB13189" />
88 <has_text text="HMDB00299" />
89 <has_text text="HMDB00191" />
90 <has_text text="HMDB00518" />
91 <has_text text="HMDB00715" />
92 <has_text text="HMDB01032" />
93 <has_text text="HMDB00208" />
94 <has_text text="HMDB04824" />
95 <has_text text="HMDB00512" />
96 <has_text text="HMDB00251" />
97 </assert_contents>
98 </output>
99 </test>
100 <test>
101 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
102 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
103 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
104 <param name="classnameColumn" value="gender"/>
105 <param name="sampleclassNames" value="M"/>
106 <param name="samplenameColumn" value="sampleMetadata"/>
107 <param name="inclusive" value="filter-in"/>
108 <param name="information" value="test-information.txt"/>
109 <output name="sampleMetadata_out">
110 <assert_contents>
111 <not_has_text text="HU_028" />
112 <not_has_text text="HU_051" />
113 <not_has_text text="HU_060" />
114 <not_has_text text="HU_110" />
115 <not_has_text text="HU_149" />
116 <not_has_text text="HU_152" />
117 <not_has_text text="HU_175" />
118 <not_has_text text="HU_178" />
119 <not_has_text text="HU_185" />
120 <not_has_text text="HU_204" />
121 <not_has_text text="HU_208" />
122 <has_text text="HU_017" />
123 <has_text text="HU_034" />
124 <has_text text="HU_078" />
125 <has_text text="HU_091" />
126 <has_text text="HU_093" />
127 <has_text text="HU_099" />
128 <has_text text="HU_130" />
129 <has_text text="HU_134" />
130 <has_text text="HU_138" />
131 </assert_contents>
132 </output>
133 </test>
134 <test>
135 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
136 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
137 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
138 <param name="classnameColumn" value="gender"/>
139 <param name="sampleclassNames" value="M"/>
140 <param name="samplenameColumn" value="sampleMetadata"/>
141 <param name="inclusive" value="filter-in"/>
142 <param name="information" value="test-information.txt"/>
143 <output name="variableMetadata_out">
144 <assert_contents>
145 <has_text text="HMDB03193" />
146 <not_has_text text="HMDB00822" />
147 <has_text text="HMDB01101" />
148 <has_text text="HMDB01101.1" />
149 <has_text text="HMDB10348" />
150 <has_text text="HMDB59717" />
151 <has_text text="HMDB13189" />
152 <has_text text="HMDB00299" />
153 <has_text text="HMDB00191" />
154 <has_text text="HMDB00518" />
155 <has_text text="HMDB00715" />
156 <has_text text="HMDB01032" />
157 <has_text text="HMDB00208" />
158 <has_text text="HMDB04824" />
159 <has_text text="HMDB00512" />
160 <has_text text="HMDB00251" />
161 </assert_contents>
162 </output>
163 </test>
164 </tests>
165
166
167
168 <help>
169
170 .. class:: infomark
171
172 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
173
174 --------------------------------------------------------------------------
175
176 .. class:: infomark
177
178 **R package**
179
180 The *w4mclassfilter* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases).
181
182 -----------------------------------------------------------------------------------------------------------------------------------------
183
184 .. class:: infomark
185
186 **Tool updates**
187
188 See the **NEWS** section at the bottom of this page
189
190 ---------------------------------------------------
191
192 ==============================================
193 Filter Workflow4Metabolomics data matrix files
194 ==============================================
195
196 -----------
197 Description
198 -----------
199
200 Filter set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample class
201
202 --------
203 Comments
204 --------
205
206 The *inclusive* parameter indicates:
207 - when 'filter-in', that only the sample-classes named should be included
208 - when 'filter-out', that all sample-classes should be included excepting the sample-classes named
209
210 -----------
211 Input files
212 -----------
213
214 +---------------------------+------------+
215 | File | Format |
216 +===========================+============+
217 | 1) Data matrix | tabular |
218 +---------------------------+------------+
219 | 2) Sample metadata | tabular |
220 +---------------------------+------------+
221 | 3) Variable metadata | tabular |
222 +---------------------------+------------+
223
224
225 ----------
226 Parameters
227 ----------
228
229 Data matrix file
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)
231 |
232
233 Sample metadata file
234 | sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
235 |
236
237 Variable metadata file
238 | variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
239 |
240
241 Names of sample classes (default = no names)
242 | comma-separated names of sample classes to include or exclude
243 |
244
245 Include named classes (default = filter-out)
246 | *filter-in* - include only the named sample classes
247 | *filter-out* - exclude only the named sample classes
248 |
249
250 Column that names the sample-class (default = 'class')
251 | name of the column in sample metadata that has the values to be tested against the 'classes' input parameter
252 |
253
254 Column that names the sample (default = 'sampleMetadata')
255 | name of the column in sample metadata that has the name of the sample
256 |
257
258
259 ------------
260 Output files
261 ------------
262
263
264 sampleMetadata_out.tabular
265 | **sampleMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for samples that have been filtered out
266 |
267
268 variableMetadata_out.tabular
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)
270 |
271
272 dataMatrix_out.tabular
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)
274 |
275
276 information.txt
277 | Text file with all messages and warnings generated during the computation
278 |
279
280 -----------------------------------------------------------------------------
281
282 ----
283 NEWS
284 ----
285
286 CHANGES IN VERSION 0.98.1
287 =========================
288
289 NEW FEATURES
290
291 First release - R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample.
292
293 *dataMatrix* *is* modified by the tool, so it *does* appear as an output file
294
295 INTERNAL MODIFICATIONS
296
297 none
298
299 </help>
300 <citations>
301 </citations>
302 </tool>
303 <!-- vim: et sw=2 ts=2 :
304 -->