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comparison w4mclassfilter.xml @ 10:649cb1bafd3e draft

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planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
author eschen42
date Thu, 09 Aug 2018 13:00:51 -0400
parents 1ced8b5dfa3e
children 9f5c0e23c205
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9:1ced8b5dfa3e 10:649cb1bafd3e
1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.9"> 1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.10">
2 <description>Filter W4m data by values or metadata</description> 2 <description>Filter W4m data by values or metadata</description>
3 3 <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation: http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/ -->
4 <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation: http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/ --> 4 <requirements>
5 5 <!-- <requirement type="package" version="6.2">readline</requirement> -->
6 <requirements> 6 <requirement type="package" version="3.4.1">r-base</requirement>
7 <!-- <requirement type="package" version="6.2">readline</requirement> --> 7 <requirement type="package" version="1.1_4">r-batch</requirement>
8 <requirement type="package" version="3.4.1">r-base</requirement> 8 <requirement type="package" version="0.98.7">w4mclassfilter</requirement>
9 <requirement type="package" version="1.1_4">r-batch</requirement> 9 </requirements>
10 <requirement type="package" version="0.98.7">w4mclassfilter</requirement> 10 <command detect_errors="aggressive"><![CDATA[
11 </requirements> 11 Rscript $__tool_directory__/w4mclassfilter_wrapper.R
12 12 dataMatrix_in '$dataMatrix_in'
13 <stdio> 13 sampleMetadata_in '$sampleMetadata_in'
14 <exit_code range="1:" level="fatal" /> 14 variableMetadata_in '$variableMetadata_in'
15 </stdio> 15 sampleclassNames '$sampleclassNames'
16 16 inclusive '$inclusive'
17 17 wildcards '$wildcards'
18 <command detect_errors="aggressive"><![CDATA[ 18 classnameColumn '$classnameColumn'
19 Rscript $__tool_directory__/w4mclassfilter_wrapper.R 19 samplenameColumn 'sampleMetadata'
20 dataMatrix_in '$dataMatrix_in' 20 variable_range_filter '$variableRangeFilter'
21 sampleMetadata_in '$sampleMetadata_in' 21 transformation '$transformation'
22 variableMetadata_in '$variableMetadata_in' 22 dataMatrix_out '$dataMatrix_out'
23 sampleclassNames '$sampleclassNames' 23 sampleMetadata_out '$sampleMetadata_out'
24 inclusive '$inclusive' 24 variableMetadata_out '$variableMetadata_out'
25 wildcards '$wildcards' 25 ]]></command>
26 classnameColumn '$classnameColumn' 26 <inputs>
27 samplenameColumn 'sampleMetadata' 27 <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"
28 variable_range_filter '$variableRangeFilter' 28 help="variables &#10006; samples" />
29 transformation '$transformation' 29 <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data"
30 dataMatrix_out '$dataMatrix_out' 30 help="sample metadata, one row per sample" />
31 sampleMetadata_out '$sampleMetadata_out' 31 <param name="variableMetadata_in" format="tabular" label="Variable metadata file" type="data"
32 variableMetadata_out '$variableMetadata_out' 32 help="variable metadata, one row per variable" />
33 ]]></command> 33 <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class"
34 34 help="name of the column in sample metadata that has the values to be tested against the 'Names of sample-classes' input parameter - defaults to 'class'">
35 <inputs> 35 <sanitizer>
36 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" /> 36 <valid initial="string.letters">
37 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" /> 37 <add preset="string.digits"/>
38 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" /> 38 <add value="&#45;" /> <!-- dash, hyphen -->
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 'Names of sample-classes' input parameter - defaults to 'class'"> 39 <add value="&#46;" /> <!-- dot, period -->
40 <sanitizer> 40 <add value="&#95;" /> <!-- underscore -->
41 <valid initial="string.letters"> 41 </valid>
42 <add preset="string.digits"/> 42 </sanitizer>
43 <add value="&#45;" /> <!-- dash, hyphen --> 43 </param>
44 <add value="&#46;" /> <!-- dot, period --> 44 <param name="sampleclassNames" label="Names of sample-classes" type="text" value = ""
45 <add value="&#95;" /> <!-- underscore --> 45 help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out; defaults to no names">
46 </valid> 46 <sanitizer>
47 </sanitizer> 47 <valid initial="string.letters">
48 </param> 48 <add preset="string.digits"/>
49 <param name="sampleclassNames" label="Names of sample-classes" type="text" value = "" help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out; defaults to no names"> 49 <add value="&#123;" /> <!-- l-cube, left-curly-bracket -->
50 <sanitizer> 50 <add value="&#124;" /> <!-- pipe -->
51 <valid initial="string.letters"> 51 <add value="&#125;" /> <!-- r-cube, right-curly-bracket -->
52 <add preset="string.digits"/> 52 <add value="&#36;" /> <!-- dollar, dollar-sign -->
53 <add value="&#123;" /> <!-- l-cube, left-curly-bracket --> 53 <add value="&#40;" /> <!-- left-paren -->
54 <add value="&#124;" /> <!-- pipe --> 54 <add value="&#41;" /> <!-- right-paren -->
55 <add value="&#125;" /> <!-- r-cube, right-curly-bracket --> 55 <add value="&#42;" /> <!-- splat, asterisk -->
56 <add value="&#36;" /> <!-- dollar, dollar-sign --> 56 <add value="&#43;" /> <!-- plus -->
57 <add value="&#40;" /> <!-- left-paren --> 57 <add value="&#45;" /> <!-- dash, hyphen -->
58 <add value="&#41;" /> <!-- right-paren --> 58 <add value="&#44;" /> <!-- comma -->
59 <add value="&#42;" /> <!-- splat, asterisk --> 59 <add value="&#46;" /> <!-- dot, period -->
60 <add value="&#43;" /> <!-- plus --> 60 <add value="&#58;" /> <!-- colon -->
61 <add value="&#45;" /> <!-- dash, hyphen --> 61 <add value="&#59;" /> <!-- semi, semicolon -->
62 <add value="&#44;" /> <!-- comma --> 62 <add value="&#63;" /> <!-- what, question mark -->
63 <add value="&#46;" /> <!-- dot, period --> 63 <add value="&#91;" /> <!-- l-squib, left-squre-bracket -->
64 <add value="&#58;" /> <!-- colon --> 64 <add value="&#92;" /> <!-- whack, backslash -->
65 <add value="&#59;" /> <!-- semi, semicolon --> 65 <add value="&#93;" /> <!-- r-squib, right-squre-bracket -->
66 <add value="&#63;" /> <!-- what, question mark --> 66 <add value="&#94;" /> <!-- hat, caret -->
67 <add value="&#91;" /> <!-- l-squib, left-squre-bracket --> 67 <add value="&#95;" /> <!-- underscore -->
68 <add value="&#92;" /> <!-- whack, backslash --> 68 </valid>
69 <add value="&#93;" /> <!-- r-squib, right-squre-bracket --> 69 </sanitizer>
70 <add value="&#94;" /> <!-- hat, caret --> 70 </param>
71 <add value="&#95;" /> <!-- underscore --> 71 <param name="wildcards" label="Use 'wild cards' or 'regular expressions'" type="select"
72 </valid> 72 help="'wild-cards' (the default) - use '*' and '?' to match class names; 'regular-expressions' - use regular expressions to match class names">
73 </sanitizer> 73 <option value="TRUE" selected="true">wild-cards</option>
74 </param> 74 <option value="FALSE">regular-expressions</option>
75 75 </param>
76 <param name="wildcards" label="Use 'wild cards' or 'regular expressions'" type="select" help="'wild-cards' (the default) - use '*' and '?' to match class names; 'regular-expressions' - use regular expressions to match class names"> 76 <param name="inclusive" label="Exclude/include named classes" type="select"
77 <option value="TRUE" selected="true">wild-cards</option> 77 help="'filter-out' (the default) - exclude only the named sample-classes; 'filter-in' - include only the named sample-classes">
78 <option value="FALSE">regular-expressions</option> 78 <option value="TRUE">filter-in</option>
79 </param> 79 <option value="FALSE" selected="true">filter-out</option>
80 <param name="inclusive" label="Exclude/include named classes" type="select" help="'filter-out' (the default) - exclude only the named sample-classes; 'filter-in' - include only the named sample-classes"> 80 </param>
81 <option value="TRUE">filter-in</option> 81 <param name="variableRangeFilter" label="Variable-range filters" type="text" value = ""
82 <option value="FALSE" selected="true">filter-out</option> 82 help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)">
83 </param> 83 <sanitizer>
84 84 <valid initial="string.letters">
85 <param name="variableRangeFilter" label="Variable-range filters" type="text" value = "" help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)"> 85 <add preset="string.digits"/>
86 <sanitizer> 86 <add value="&#44;" /> <!-- comma -->
87 <valid initial="string.letters"> 87 <add value="&#45;" /> <!-- dash, hyphen -->
88 <add preset="string.digits"/> 88 <add value="&#46;" /> <!-- dot, period -->
89 <add value="&#44;" /> <!-- comma --> 89 <add value="&#58;" /> <!-- colon -->
90 <add value="&#45;" /> <!-- dash, hyphen --> 90 <add value="&#95;" /> <!-- underscore -->
91 <add value="&#46;" /> <!-- dot, period --> 91 </valid>
92 <add value="&#58;" /> <!-- colon --> 92 </sanitizer>
93 <add value="&#95;" /> <!-- underscore --> 93 </param>
94 </valid> 94 <param name="transformation" label="Data-transformation" type="select"
95 </sanitizer> 95 help="'none' (the default) - do not transform data; 'log2' - log base 2 of data; 'log10' - log base 10 of data; in all cases, negative and missing values are imputed to zero">
96 </param> 96 <option value="none" selected="true">none</option>
97 <param name="transformation" label="Data-transformation" type="select" help="'none' (the default) - do not transform data; 'log2' - log base 2 of data; 'log10' - log base 10 of data; in all cases, negative and missing values are imputed to zero"> 97 <option value="log2">log2</option>
98 <option value="none" selected="true">none</option> 98 <option value="log10">log10</option>
99 <option value="log2">log2</option> 99 </param>
100 <option value="log10">log10</option> 100 </inputs>
101 </param> 101 <outputs>
102 102 <data name="dataMatrix_out" format="tabular" label="${dataMatrix_in.name}.subset" ></data>
103 </inputs> 103 <data name="sampleMetadata_out" format="tabular" label="${sampleMetadata_in.name}.subset" ></data>
104 <outputs> 104 <data name="variableMetadata_out" format="tabular" label="${variableMetadata_in.name}.subset" ></data>
105 <data name="dataMatrix_out" label="${dataMatrix_in.name}.subset" format="tabular" ></data> 105 </outputs>
106 <data name="sampleMetadata_out" label="${sampleMetadata_in.name}.subset" format="tabular" ></data> 106 <tests>
107 <data name="variableMetadata_out" label="${variableMetadata_in.name}.subset" format="tabular" ></data> 107 <!-- test 1 -->
108 </outputs> 108 <test>
109 109 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
110 <tests> 110 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
111 <test> 111 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
112 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 112 <param name="classnameColumn" value="gender"/>
113 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 113 <param name="sampleclassNames" value="M"/>
114 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 114 <param name="wildcards" value="FALSE"/>
115 <param name="classnameColumn" value="gender"/> 115 <param name="inclusive" value="filter-in"/>
116 <param name="sampleclassNames" value="M"/> 116 <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/>
117 <param name="wildcards" value="FALSE"/> 117 <param name="transformation" value="log10"/>
118 <param name="inclusive" value="filter-in"/> 118 <output name="dataMatrix_out">
119 <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/> 119 <assert_contents>
120 <param name="transformation" value="log10"/> 120 <has_text text="5.87336711011293" />
121 <output name="dataMatrix_out"> 121 </assert_contents>
122 <assert_contents> 122 </output>
123 <has_text text="5.87336711011293" /> 123 <output name="sampleMetadata_out">
124 </assert_contents> 124 <assert_contents>
125 </output> 125 <not_has_text text="HU_028" />
126 <output name="sampleMetadata_out"> 126 <not_has_text text="HU_051" />
127 <assert_contents> 127 <not_has_text text="HU_060" />
128 <not_has_text text="HU_028" /> 128 <not_has_text text="HU_110" />
129 <not_has_text text="HU_051" /> 129 <not_has_text text="HU_149" />
130 <not_has_text text="HU_060" /> 130 <not_has_text text="HU_152" />
131 <not_has_text text="HU_110" /> 131 <not_has_text text="HU_175" />
132 <not_has_text text="HU_149" /> 132 <not_has_text text="HU_178" />
133 <not_has_text text="HU_152" /> 133 <not_has_text text="HU_185" />
134 <not_has_text text="HU_175" /> 134 <not_has_text text="HU_204" />
135 <not_has_text text="HU_178" /> 135 <not_has_text text="HU_208" />
136 <not_has_text text="HU_185" /> 136 <has_text text="HU_017" />
137 <not_has_text text="HU_204" /> 137 <has_text text="HU_034" />
138 <not_has_text text="HU_208" /> 138 <has_text text="HU_078" />
139 <has_text text="HU_017" /> 139 <has_text text="HU_091" />
140 <has_text text="HU_034" /> 140 <has_text text="HU_093" />
141 <has_text text="HU_078" /> 141 <has_text text="HU_099" />
142 <has_text text="HU_091" /> 142 <has_text text="HU_130" />
143 <has_text text="HU_093" /> 143 <has_text text="HU_134" />
144 <has_text text="HU_099" /> 144 <has_text text="HU_138" />
145 <has_text text="HU_130" /> 145 </assert_contents>
146 <has_text text="HU_134" /> 146 </output>
147 <has_text text="HU_138" /> 147 <output name="variableMetadata_out">
148 </assert_contents> 148 <assert_contents>
149 </output> 149 <not_has_text text="HMDB00191" />
150 <output name="variableMetadata_out"> 150 <has_text text="HMDB00208" />
151 <assert_contents> 151 <not_has_text text="HMDB00251" />
152 <not_has_text text="HMDB00191" /> 152 <not_has_text text="HMDB00299" />
153 <has_text text="HMDB00208" /> 153 <not_has_text text="HMDB00512" />
154 <not_has_text text="HMDB00251" /> 154 <not_has_text text="HMDB00518" />
155 <not_has_text text="HMDB00299" /> 155 <not_has_text text="HMDB00715" />
156 <not_has_text text="HMDB00512" /> 156 <not_has_text text="HMDB00822" />
157 <not_has_text text="HMDB00518" /> 157 <has_text text="HMDB01032" />
158 <not_has_text text="HMDB00715" /> 158 <has_text text="HMDB01101.1" />
159 <not_has_text text="HMDB00822" /> 159 <not_has_text text="HMDB03193" />
160 <has_text text="HMDB01032" /> 160 <not_has_text text="HMDB04824" />
161 <has_text text="HMDB01101.1" /> 161 <not_has_text text="HMDB10348" />
162 <not_has_text text="HMDB03193" /> 162 <has_text text="HMDB13189" />
163 <not_has_text text="HMDB04824" /> 163 <not_has_text text="HMDB59717" />
164 <not_has_text text="HMDB10348" /> 164 </assert_contents>
165 <has_text text="HMDB13189" /> 165 </output>
166 <not_has_text text="HMDB59717" /> 166 </test>
167 </assert_contents> 167 <!-- test 2 -->
168 </output> 168 <test>
169 </test> 169 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
170 <test> 170 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
171 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 171 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
172 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 172 <param name="classnameColumn" value="sampleMetadata"/>
173 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 173 <!-- test that hyphens in regular expressions work -->
174 <param name="classnameColumn" value="sampleMetadata"/> 174 <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/>
175 <!-- test that hyphens in regular expressions work --> 175 <param name="wildcards" value="FALSE"/>
176 <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/> 176 <param name="inclusive" value="filter-in"/>
177 <param name="wildcards" value="FALSE"/> 177 <param name="variableRangeFilter" value="FEATMAX:20.93157:,mz:200:,rt::800"/>
178 <param name="inclusive" value="filter-in"/> 178 <param name="transformation" value="log2"/>
179 <param name="variableRangeFilter" value="FEATMAX:20.93157:,mz:200:,rt::800"/> 179 <output name="dataMatrix_out">
180 <param name="transformation" value="log2"/> 180 <assert_contents>
181 <output name="dataMatrix_out"> 181 <has_text text="19.5109032146715" />
182 <assert_contents> 182 </assert_contents>
183 <has_text text="19.5109032146715" /> 183 </output>
184 </assert_contents> 184 <output name="sampleMetadata_out">
185 </output> 185 <assert_contents>
186 <output name="sampleMetadata_out"> 186 <has_text text="HU_028" />
187 <assert_contents> 187 <has_text text="HU_051" />
188 <has_text text="HU_028" /> 188 <has_text text="HU_060" />
189 <has_text text="HU_051" /> 189 <has_text text="HU_110" />
190 <has_text text="HU_060" /> 190 <has_text text="HU_149" />
191 <has_text text="HU_110" /> 191 <has_text text="HU_152" />
192 <has_text text="HU_149" /> 192 <has_text text="HU_175" />
193 <has_text text="HU_152" /> 193 <has_text text="HU_178" />
194 <has_text text="HU_175" /> 194 <has_text text="HU_185" />
195 <has_text text="HU_178" /> 195 <not_has_text text="HU_204" />
196 <has_text text="HU_185" /> 196 <has_text text="HU_208" />
197 <not_has_text text="HU_204" /> 197 <has_text text="HU_017" />
198 <has_text text="HU_208" /> 198 <has_text text="HU_034" />
199 <has_text text="HU_017" /> 199 <has_text text="HU_078" />
200 <has_text text="HU_034" /> 200 <has_text text="HU_091" />
201 <has_text text="HU_078" /> 201 <has_text text="HU_093" />
202 <has_text text="HU_091" /> 202 <has_text text="HU_099" />
203 <has_text text="HU_093" /> 203 <has_text text="HU_130" />
204 <has_text text="HU_099" /> 204 <has_text text="HU_134" />
205 <has_text text="HU_130" /> 205 <has_text text="HU_138" />
206 <has_text text="HU_134" /> 206 </assert_contents>
207 <has_text text="HU_138" /> 207 </output>
208 </assert_contents> 208 <output name="variableMetadata_out">
209 </output> 209 <assert_contents>
210 <output name="variableMetadata_out"> 210 <has_text text="HMDB00191" />
211 <assert_contents> 211 <has_text text="HMDB00208" />
212 <has_text text="HMDB00191" /> 212 <not_has_text text="HMDB00251" />
213 <has_text text="HMDB00208" /> 213 <not_has_text text="HMDB00299" />
214 <not_has_text text="HMDB00251" /> 214 <not_has_text text="HMDB00512" />
215 <not_has_text text="HMDB00299" /> 215 <not_has_text text="HMDB00518" />
216 <not_has_text text="HMDB00512" /> 216 <not_has_text text="HMDB00715" />
217 <not_has_text text="HMDB00518" /> 217 <not_has_text text="HMDB00822" />
218 <not_has_text text="HMDB00715" /> 218 <has_text text="HMDB01032" />
219 <not_has_text text="HMDB00822" /> 219 <has_text text="HMDB01101.1" />
220 <has_text text="HMDB01032" /> 220 <not_has_text text="HMDB03193" />
221 <has_text text="HMDB01101.1" /> 221 <not_has_text text="HMDB04824" />
222 <not_has_text text="HMDB03193" /> 222 <not_has_text text="HMDB10348" />
223 <not_has_text text="HMDB04824" /> 223 <has_text text="HMDB13189" />
224 <not_has_text text="HMDB10348" /> 224 <not_has_text text="HMDB59717" />
225 <has_text text="HMDB13189" /> 225 </assert_contents>
226 <not_has_text text="HMDB59717" /> 226 </output>
227 </assert_contents> 227 </test>
228 </output> 228 <!-- test 3 -->
229 </test> 229 <test>
230 <test> 230 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
231 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 231 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
232 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 232 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
233 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 233 <param name="classnameColumn" value="gender"/>
234 <param name="classnameColumn" value="gender"/> 234 <param name="sampleclassNames" value="M"/>
235 <param name="sampleclassNames" value="M"/> 235 <param name="inclusive" value="filter-in"/>
236 <param name="inclusive" value="filter-in"/> 236 <param name="transformation" value="none"/>
237 <param name="transformation" value="none"/> 237 <output name="dataMatrix_out">
238 <output name="dataMatrix_out"> 238 <assert_contents>
239 <assert_contents> 239 <not_has_text text="HU_028" />
240 <not_has_text text="HU_028" /> 240 <not_has_text text="HU_051" />
241 <not_has_text text="HU_051" /> 241 <not_has_text text="HU_060" />
242 <not_has_text text="HU_060" /> 242 <not_has_text text="HU_110" />
243 <not_has_text text="HU_110" /> 243 <not_has_text text="HU_149" />
244 <not_has_text text="HU_149" /> 244 <not_has_text text="HU_152" />
245 <not_has_text text="HU_152" /> 245 <not_has_text text="HU_175" />
246 <not_has_text text="HU_175" /> 246 <not_has_text text="HU_178" />
247 <not_has_text text="HU_178" /> 247 <not_has_text text="HU_185" />
248 <not_has_text text="HU_185" /> 248 <not_has_text text="HU_204" />
249 <not_has_text text="HU_204" /> 249 <not_has_text text="HU_208" />
250 <not_has_text text="HU_208" /> 250 <has_text text="HU_017" />
251 <has_text text="HU_017" /> 251 <has_text text="HU_034" />
252 <has_text text="HU_034" /> 252 <has_text text="HU_078" />
253 <has_text text="HU_078" /> 253 <has_text text="HU_091" />
254 <has_text text="HU_091" /> 254 <has_text text="HU_093" />
255 <has_text text="HU_093" /> 255 <has_text text="HU_099" />
256 <has_text text="HU_099" /> 256 <has_text text="HU_130" />
257 <has_text text="HU_130" /> 257 <has_text text="HU_134" />
258 <has_text text="HU_134" /> 258 <has_text text="HU_138" />
259 <has_text text="HU_138" /> 259 <has_text text="HMDB03193" />
260 <has_text text="HMDB03193" /> 260 <not_has_text text="HMDB00822" />
261 <not_has_text text="HMDB00822" /> 261 <has_text text="HMDB01101" />
262 <has_text text="HMDB01101" /> 262 <has_text text="HMDB01101.1" />
263 <has_text text="HMDB01101.1" /> 263 <has_text text="HMDB10348" />
264 <has_text text="HMDB10348" /> 264 <has_text text="HMDB59717" />
265 <has_text text="HMDB59717" /> 265 <has_text text="HMDB13189" />
266 <has_text text="HMDB13189" /> 266 <has_text text="HMDB00299" />
267 <has_text text="HMDB00299" /> 267 <has_text text="HMDB00191" />
268 <has_text text="HMDB00191" /> 268 <has_text text="HMDB00518" />
269 <has_text text="HMDB00518" /> 269 <has_text text="HMDB00715" />
270 <has_text text="HMDB00715" /> 270 <has_text text="HMDB01032" />
271 <has_text text="HMDB01032" /> 271 <has_text text="HMDB00208" />
272 <has_text text="HMDB00208" /> 272 <has_text text="HMDB04824" />
273 <has_text text="HMDB04824" /> 273 <has_text text="HMDB00512" />
274 <has_text text="HMDB00512" /> 274 <has_text text="HMDB00251" />
275 <has_text text="HMDB00251" /> 275 </assert_contents>
276 </assert_contents> 276 </output>
277 </output> 277 </test>
278 </test> 278 <!-- test 4 -->
279 <test> 279 <test>
280 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 280 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
281 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 281 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
282 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 282 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
283 <param name="classnameColumn" value="gender"/> 283 <param name="classnameColumn" value="gender"/>
284 <param name="sampleclassNames" value="*"/> 284 <param name="sampleclassNames" value="*"/>
285 <param name="wildcards" value="TRUE"/> 285 <param name="wildcards" value="TRUE"/>
286 <param name="inclusive" value="filter-in"/> 286 <param name="inclusive" value="filter-in"/>
287 <output name="sampleMetadata_out"> 287 <output name="sampleMetadata_out">
288 <assert_contents> 288 <assert_contents>
289 <not_has_text text="HU_204" /> 289 <not_has_text text="HU_204" />
290 <has_text text="HU_028" /> 290 <has_text text="HU_028" />
291 <has_text text="HU_051" /> 291 <has_text text="HU_051" />
292 <has_text text="HU_060" /> 292 <has_text text="HU_060" />
293 <has_text text="HU_110" /> 293 <has_text text="HU_110" />
294 <has_text text="HU_149" /> 294 <has_text text="HU_149" />
295 <has_text text="HU_152" /> 295 <has_text text="HU_152" />
296 <has_text text="HU_175" /> 296 <has_text text="HU_175" />
297 <has_text text="HU_178" /> 297 <has_text text="HU_178" />
298 <has_text text="HU_185" /> 298 <has_text text="HU_185" />
299 <has_text text="HU_208" /> 299 <has_text text="HU_208" />
300 <has_text text="HU_017" /> 300 <has_text text="HU_017" />
301 <has_text text="HU_034" /> 301 <has_text text="HU_034" />
302 <has_text text="HU_078" /> 302 <has_text text="HU_078" />
303 <has_text text="HU_091" /> 303 <has_text text="HU_091" />
304 <has_text text="HU_093" /> 304 <has_text text="HU_093" />
305 <has_text text="HU_099" /> 305 <has_text text="HU_099" />
306 <has_text text="HU_130" /> 306 <has_text text="HU_130" />
307 <has_text text="HU_134" /> 307 <has_text text="HU_134" />
308 <has_text text="HU_138" /> 308 <has_text text="HU_138" />
309 </assert_contents> 309 </assert_contents>
310 </output> 310 </output>
311 </test> 311 </test>
312 <test> 312 <!-- test 5 -->
313 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 313 <test>
314 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 314 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
315 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 315 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
316 <param name="classnameColumn" value="gender"/> 316 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
317 <param name="sampleclassNames" value="M"/> 317 <param name="classnameColumn" value="gender"/>
318 <param name="wildcards" value="FALSE"/> 318 <param name="sampleclassNames" value="M"/>
319 <param name="inclusive" value="filter-in"/> 319 <param name="wildcards" value="FALSE"/>
320 <output name="sampleMetadata_out"> 320 <param name="inclusive" value="filter-in"/>
321 <assert_contents> 321 <output name="sampleMetadata_out">
322 <not_has_text text="HU_028" /> 322 <assert_contents>
323 <not_has_text text="HU_051" /> 323 <not_has_text text="HU_028" />
324 <not_has_text text="HU_060" /> 324 <not_has_text text="HU_051" />
325 <not_has_text text="HU_110" /> 325 <not_has_text text="HU_060" />
326 <not_has_text text="HU_149" /> 326 <not_has_text text="HU_110" />
327 <not_has_text text="HU_152" /> 327 <not_has_text text="HU_149" />
328 <not_has_text text="HU_175" /> 328 <not_has_text text="HU_152" />
329 <not_has_text text="HU_178" /> 329 <not_has_text text="HU_175" />
330 <not_has_text text="HU_185" /> 330 <not_has_text text="HU_178" />
331 <not_has_text text="HU_204" /> 331 <not_has_text text="HU_185" />
332 <not_has_text text="HU_208" /> 332 <not_has_text text="HU_204" />
333 <has_text text="HU_017" /> 333 <not_has_text text="HU_208" />
334 <has_text text="HU_034" /> 334 <has_text text="HU_017" />
335 <has_text text="HU_078" /> 335 <has_text text="HU_034" />
336 <has_text text="HU_091" /> 336 <has_text text="HU_078" />
337 <has_text text="HU_093" /> 337 <has_text text="HU_091" />
338 <has_text text="HU_099" /> 338 <has_text text="HU_093" />
339 <has_text text="HU_130" /> 339 <has_text text="HU_099" />
340 <has_text text="HU_134" /> 340 <has_text text="HU_130" />
341 <has_text text="HU_138" /> 341 <has_text text="HU_134" />
342 </assert_contents> 342 <has_text text="HU_138" />
343 </output> 343 </assert_contents>
344 </test> 344 </output>
345 <test> 345 </test>
346 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 346 <!-- test 6 -->
347 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 347 <test>
348 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 348 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
349 <param name="classnameColumn" value="gender"/> 349 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
350 <param name="sampleclassNames" value="M"/> 350 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
351 <param name="wildcards" value="FALSE"/> 351 <param name="classnameColumn" value="gender"/>
352 <param name="inclusive" value="filter-in"/> 352 <param name="sampleclassNames" value="M"/>
353 <output name="variableMetadata_out"> 353 <param name="wildcards" value="FALSE"/>
354 <assert_contents> 354 <param name="inclusive" value="filter-in"/>
355 <has_text text="HMDB03193" /> 355 <output name="variableMetadata_out">
356 <not_has_text text="HMDB00822" /> 356 <assert_contents>
357 <has_text text="HMDB01101" /> 357 <has_text text="HMDB03193" />
358 <has_text text="HMDB01101.1" /> 358 <not_has_text text="HMDB00822" />
359 <has_text text="HMDB10348" /> 359 <has_text text="HMDB01101" />
360 <has_text text="HMDB59717" /> 360 <has_text text="HMDB01101.1" />
361 <has_text text="HMDB13189" /> 361 <has_text text="HMDB10348" />
362 <has_text text="HMDB00299" /> 362 <has_text text="HMDB59717" />
363 <has_text text="HMDB00191" /> 363 <has_text text="HMDB13189" />
364 <has_text text="HMDB00518" /> 364 <has_text text="HMDB00299" />
365 <has_text text="HMDB00715" /> 365 <has_text text="HMDB00191" />
366 <has_text text="HMDB01032" /> 366 <has_text text="HMDB00518" />
367 <has_text text="HMDB00208" /> 367 <has_text text="HMDB00715" />
368 <has_text text="HMDB04824" /> 368 <has_text text="HMDB01032" />
369 <has_text text="HMDB00512" /> 369 <has_text text="HMDB00208" />
370 <has_text text="HMDB00251" /> 370 <has_text text="HMDB04824" />
371 </assert_contents> 371 <has_text text="HMDB00512" />
372 </output> 372 <has_text text="HMDB00251" />
373 </test> 373 </assert_contents>
374 <test> 374 </output>
375 <param name="dataMatrix_in" value="input_nofilter_dataMatrix.tsv"/> 375 </test>
376 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 376 <!-- test 7 -->
377 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 377 <test>
378 <param name="classnameColumn" value="gender"/> 378 <param name="dataMatrix_in" value="input_nofilter_dataMatrix.tsv"/>
379 <param name="sampleclassNames" value="M"/> 379 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
380 <param name="wildcards" value="FALSE"/> 380 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
381 <param name="inclusive" value="filter-in"/> 381 <param name="classnameColumn" value="gender"/>
382 <output name="variableMetadata_out"> 382 <param name="sampleclassNames" value="M"/>
383 <assert_contents> 383 <param name="wildcards" value="FALSE"/>
384 <has_text text="HMDB03193" /> 384 <param name="inclusive" value="filter-in"/>
385 <not_has_text text="HMDB00822" /> 385 <output name="variableMetadata_out">
386 <has_text text="HMDB01101" /> 386 <assert_contents>
387 <has_text text="HMDB01101.1" /> 387 <has_text text="HMDB03193" />
388 <has_text text="HMDB10348" /> 388 <not_has_text text="HMDB00822" />
389 <has_text text="HMDB59717" /> 389 <has_text text="HMDB01101" />
390 <not_has_text text="HMDB13189" /> 390 <has_text text="HMDB01101.1" />
391 <has_text text="HMDB00299" /> 391 <has_text text="HMDB10348" />
392 <has_text text="HMDB00191" /> 392 <has_text text="HMDB59717" />
393 <has_text text="HMDB00518" /> 393 <not_has_text text="HMDB13189" />
394 <has_text text="HMDB00715" /> 394 <has_text text="HMDB00299" />
395 <has_text text="HMDB01032" /> 395 <has_text text="HMDB00191" />
396 <has_text text="HMDB00208" /> 396 <has_text text="HMDB00518" />
397 <has_text text="HMDB04824" /> 397 <has_text text="HMDB00715" />
398 <has_text text="HMDB00512" /> 398 <has_text text="HMDB01032" />
399 <has_text text="HMDB00251" /> 399 <has_text text="HMDB00208" />
400 </assert_contents> 400 <has_text text="HMDB04824" />
401 </output> 401 <has_text text="HMDB00512" />
402 </test> 402 <has_text text="HMDB00251" />
403 <test> 403 </assert_contents>
404 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 404 </output>
405 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 405 </test>
406 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 406 <!-- test 8 -->
407 <param name="classnameColumn" value="gender"/> 407 <test>
408 <param name="sampleclassNames" value="[Mm],[fF]"/> 408 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
409 <param name="wildcards" value="FALSE"/> 409 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
410 <param name="inclusive" value="filter-in"/> 410 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
411 <output name="sampleMetadata_out"> 411 <param name="classnameColumn" value="gender"/>
412 <assert_contents> 412 <param name="sampleclassNames" value="[Mm],[fF]"/>
413 <has_text text="HU_028" /> 413 <param name="wildcards" value="FALSE"/>
414 <has_text text="HU_051" /> 414 <param name="inclusive" value="filter-in"/>
415 <has_text text="HU_060" /> 415 <output name="sampleMetadata_out">
416 <has_text text="HU_110" /> 416 <assert_contents>
417 <has_text text="HU_149" /> 417 <has_text text="HU_028" />
418 <has_text text="HU_152" /> 418 <has_text text="HU_051" />
419 <has_text text="HU_175" /> 419 <has_text text="HU_060" />
420 <has_text text="HU_178" /> 420 <has_text text="HU_110" />
421 <has_text text="HU_185" /> 421 <has_text text="HU_149" />
422 <not_has_text text="HU_204" /> 422 <has_text text="HU_152" />
423 <has_text text="HU_208" /> 423 <has_text text="HU_175" />
424 <has_text text="HU_017" /> 424 <has_text text="HU_178" />
425 <has_text text="HU_034" /> 425 <has_text text="HU_185" />
426 <has_text text="HU_078" /> 426 <not_has_text text="HU_204" />
427 <has_text text="HU_091" /> 427 <has_text text="HU_208" />
428 <has_text text="HU_093" /> 428 <has_text text="HU_017" />
429 <has_text text="HU_099" /> 429 <has_text text="HU_034" />
430 <has_text text="HU_130" /> 430 <has_text text="HU_078" />
431 <has_text text="HU_134" /> 431 <has_text text="HU_091" />
432 <has_text text="HU_138" /> 432 <has_text text="HU_093" />
433 </assert_contents> 433 <has_text text="HU_099" />
434 </output> 434 <has_text text="HU_130" />
435 </test> 435 <has_text text="HU_134" />
436 <test> 436 <has_text text="HU_138" />
437 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 437 </assert_contents>
438 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 438 </output>
439 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 439 </test>
440 <param name="classnameColumn" value=""/> 440 <!-- test 9 -->
441 <param name="sampleclassNames" value="M"/> 441 <test>
442 <param name="wildcards" value="FALSE"/> 442 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
443 <param name="inclusive" value="filter-in"/> 443 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
444 <output name="sampleMetadata_out"> 444 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
445 <assert_contents> 445 <param name="classnameColumn" value=""/>
446 <has_text text="HU_028" /> 446 <param name="sampleclassNames" value="M"/>
447 <has_text text="HU_051" /> 447 <param name="wildcards" value="FALSE"/>
448 <has_text text="HU_060" /> 448 <param name="inclusive" value="filter-in"/>
449 <has_text text="HU_110" /> 449 <output name="sampleMetadata_out">
450 <has_text text="HU_149" /> 450 <assert_contents>
451 <has_text text="HU_152" /> 451 <has_text text="HU_028" />
452 <has_text text="HU_175" /> 452 <has_text text="HU_051" />
453 <has_text text="HU_178" /> 453 <has_text text="HU_060" />
454 <has_text text="HU_185" /> 454 <has_text text="HU_110" />
455 <not_has_text text="HU_204" /> 455 <has_text text="HU_149" />
456 <has_text text="HU_208" /> 456 <has_text text="HU_152" />
457 <has_text text="HU_017" /> 457 <has_text text="HU_175" />
458 <has_text text="HU_034" /> 458 <has_text text="HU_178" />
459 <has_text text="HU_078" /> 459 <has_text text="HU_185" />
460 <has_text text="HU_091" /> 460 <not_has_text text="HU_204" />
461 <has_text text="HU_093" /> 461 <has_text text="HU_208" />
462 <has_text text="HU_099" /> 462 <has_text text="HU_017" />
463 <has_text text="HU_130" /> 463 <has_text text="HU_034" />
464 <has_text text="HU_134" /> 464 <has_text text="HU_078" />
465 <has_text text="HU_138" /> 465 <has_text text="HU_091" />
466 </assert_contents> 466 <has_text text="HU_093" />
467 </output> 467 <has_text text="HU_099" />
468 </test> 468 <has_text text="HU_130" />
469 </tests> 469 <has_text text="HU_134" />
470 470 <has_text text="HU_138" />
471 471 </assert_contents>
472 472 </output>
473 <help><![CDATA[ 473 </test>
474 </tests>
475 <help><![CDATA[
474 476
475 477
476 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu) 478 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
477 479
478 -------------------------------------------------------------------------- 480 --------------------------------------------------------------------------
502 GC-MS and LC-MS experiments seek to resolve as features chemicals that have distinct chromatographic retention-time ("rt") and (after ionization) mass-to-charge ratio ("m/z" or "mz"). 504 GC-MS and LC-MS experiments seek to resolve as features chemicals that have distinct chromatographic retention-time ("rt") and (after ionization) mass-to-charge ratio ("m/z" or "mz").
503 (If the MS protocol includes fragmentation, several features may result for each chemical.) 505 (If the MS protocol includes fragmentation, several features may result for each chemical.)
504 Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of rt and m/z. 506 Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of rt and m/z.
505 Ideally, features would be sufficiently reproducible among sample-runs to distinguish features that are commmon among samples from those that differ. 507 Ideally, features would be sufficiently reproducible among sample-runs to distinguish features that are commmon among samples from those that differ.
506 508
507 The chromatographic retention-time for a chemical can vary from one chromatography run to the next. 509 The chromatographic retention-time for a chemical can vary from one chromatography run to the next.
508 Workflow4Metabolomics (W4m, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017]) is a "flavor" of Galaxy that uses the XCMS preprocessing tools for "retention-time correction" to align features among samples. 510 Workflow4Metabolomics (W4m, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017]) is a "flavor" of Galaxy that uses the XCMS preprocessing tools for "retention-time correction" to align features among samples.
509 Features may be better aligned if pooled samples and blanks are included. 511 Features may be better aligned if pooled samples and blanks are included.
510 512
511 Multivariate statistical techniques may be used to discover clusters of similar samples (Th]]>&#233;<![CDATA[venot *et al.*, 2015). 513 Multivariate statistical techniques may be used to discover clusters of similar samples (Th]]>&#233;<![CDATA[venot *et al.*, 2015).
512 However, once retention-time alignment of features has been achieved among samples in GC-MS and LC-MS datasets: 514 However, once retention-time alignment of features has been achieved among samples in GC-MS and LC-MS datasets:
699 701
700 - the **name of a column of `variableMetadata`** which must have numerical data (e.g., "mz"); 702 - the **name of a column of `variableMetadata`** which must have numerical data (e.g., "mz");
701 - the **minimum allowed value** in that column for the feature to be retained (e.g., 200); 703 - the **minimum allowed value** in that column for the feature to be retained (e.g., 200);
702 - the **maximum allowed value** (e.g., 800). 704 - the **maximum allowed value** (e.g., 800).
703 705
704 Note for the range specification strings: 706 Note for the range specification strings:
705 707
706 - **If the "maximum" is less than the "minimum", then the range is exclusive** (e.g., "mz:800:200" means retain only features whose mz is NOT in the range 200-800) 708 - **If the "maximum" is less than the "minimum", then the range is exclusive** (e.g., "mz:800:200" means retain only features whose mz is NOT in the range 200-800)
707 - **If the name supplied in the first field is 'FEATMAX',** then the string is defining the minimum (and possibly, though less useful, maximum) intensity for each feature in the dataMatrix. For example, "FEATMAX:1e6:" would specify that any feature would be excluded if no sample had an intensity for that feature greater than 1000000. 709 - **If the name supplied in the first field is 'FEATMAX',** then the string is defining the minimum (and possibly, though less useful, maximum) intensity for each feature in the dataMatrix. For example, "FEATMAX:1e6:" would specify that any feature would be excluded if no sample had an intensity for that feature greater than 1000000.
708 710
709 - Note, however, that when the "maximum" is greater than the "minimum" for the FEATMAX range specification, then the specification is ignored. 711 - Note, however, that when the "maximum" is greater than the "minimum" for the FEATMAX range specification, then the specification is ignored.
718 720
719 ----------- 721 -----------
720 Input Files 722 Input Files
721 ----------- 723 -----------
722 724
723 +------------------------------------------------------------------------------------------------------------------------+ 725 +------------------------------------------------------------------------------------------------------------------------------------------------------+
724 | Input File URL | 726 | Input File URL |
725 +========================================================================================================================+ 727 +======================================================================================================================================================+
726 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_dataMatrix.tsv | 728 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_dataMatrix.tsv |
727 +------------------------------------------------------------------------------------------------------------------------+ 729 +------------------------------------------------------------------------------------------------------------------------------------------------------+
728 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_sampleMetadata.tsv | 730 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_sampleMetadata.tsv |
729 +------------------------------------------------------------------------------------------------------------------------+ 731 +------------------------------------------------------------------------------------------------------------------------------------------------------+
730 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_variableMetadata.tsv | 732 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_variableMetadata.tsv |
731 +------------------------------------------------------------------------------------------------------------------------+ 733 +------------------------------------------------------------------------------------------------------------------------------------------------------+
732 734
733 .. class:: infomark 735 .. class:: infomark
734 736
735 ------------------------------- 737 -------------------------------
736 Running Without Range-Filtering 738 Running Without Range-Filtering
754 | Data transforamtion | none | 756 | Data transforamtion | none |
755 +------------------------------------+-------------------------------+ 757 +------------------------------------+-------------------------------+
756 758
757 **Expected outputs** 759 **Expected outputs**
758 760
759 +-------------------+---------------------------------------------------------------------------------------------------------------------------+ 761 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
760 | Expected Output | Download from URL | 762 | Expected Output | Download from URL |
761 +===================+===========================================================================================================================+ 763 +===================+=================================================================================================================================================+
762 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_dataMatrix.tsv | 764 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_dataMatrix.tsv |
763 +-------------------+---------------------------------------------------------------------------------------------------------------------------+ 765 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
764 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_sampleMetadata.tsv | 766 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_sampleMetadata.tsv |
765 +-------------------+---------------------------------------------------------------------------------------------------------------------------+ 767 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
766 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_variableMetadata.tsv | 768 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_variableMetadata.tsv |
767 +-------------------+---------------------------------------------------------------------------------------------------------------------------+ 769 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
768 770
769 .. class:: infomark 771 .. class:: infomark
770 772
771 ---------------------------- 773 ----------------------------
772 Running With Range-Filtering 774 Running With Range-Filtering
791 | Data transforamtion | log2 | 793 | Data transforamtion | log2 |
792 +------------------------------------+------------------------------------+ 794 +------------------------------------+------------------------------------+
793 795
794 **Expected outputs** 796 **Expected outputs**
795 797
796 +-------------------+------------------------------------------------------------------------------------------------------------------------------+ 798 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
797 | Expected Output | Download from URL | 799 | Expected Output | Download from URL |
798 +===================+==============================================================================================================================+ 800 +===================+===================================================================================================================================================+
799 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_dataMatrix.tsv | 801 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_dataMatrix.tsv |
800 +-------------------+------------------------------------------------------------------------------------------------------------------------------+ 802 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
801 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_sampleMetadata.tsv | 803 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_sampleMetadata.tsv |
802 +-------------------+------------------------------------------------------------------------------------------------------------------------------+ 804 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
803 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_variableMetadata.tsv | 805 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv |
804 +-------------------+------------------------------------------------------------------------------------------------------------------------------+ 806 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
805 807 ]]></help>
806 ----------------------------------------------------------------------------- 808 <citations>
807 809 <!-- Giacomoni_2014 W4m 2.5 -->
808 ---- 810 <citation type="doi">10.1093/bioinformatics/btu813</citation>
809 NEWS 811 <!-- Guitton_2017 W4m 3.0 -->
810 ---- 812 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
811 813 <!-- Kuhl_2012 CAMERA -->
812 Changes in version 0.98.9 814 <citation type="doi">10.1021/ac202450g</citation>
813 ========================= 815 <!-- Smith_2006 XCMS -->
814 816 <citation type="doi">10.1021/ac051437y</citation>
815 New features 817 <!-- Thevenot_2015 Urinary metabolome statistics -->
816 818 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
817 - Fixed bug. 819 </citations>
818 820 <!--
819 Internal modifications 821 vim:noet:sw=4:ts=4
820
821 - Added the hyphen to the characters permitted within regular expressions.
822
823 Changes in version 0.98.8
824 =========================
825
826 New features
827
828 - The tool now appears in Galaxy with a new, more representative name: "W4m Data Subset". (Earlier versions of this tool appeared in Galaxy with the name "Sample Subset".)
829 - Option was added to log-transform data matrix values.
830 - Output datasets are named in conformance with the W4m convention of appending the name of each preprocessing tool to the input dataset name.
831 - Superflous "Column that names the sample" input parameter was eliminated.
832 - Some documentation was updated or clarified.
833
834 Internal modifications
835
836 - None
837
838 Changes in version 0.98.7
839 =========================
840
841 New features
842
843 - First column of output variableMetadata (that has feature names) now is always named "variableMetadata".
844 - First column of output sampleMetadata now (that has sample names) now is always named "sampleMetadata".
845
846 Internal modifications
847
848 - Now uses w4mclassfilter R package v0.98.7.
849
850 Changes in version 0.98.6
851 =========================
852
853 New features
854
855 - Added support for filtering out features whose attributes fall outside specified ranges.
856 For more detail, see "Variable-range filters" above.
857
858 Internal modifications
859
860 - Now uses w4mclassfilter R package v0.98.6.
861 - Now sorts sample names and feature names in output files because some statistical tools expect the same order in `dataMatrix` row and column names as in the corresponding metadata files.
862
863 Changes in version 0.98.3
864 =========================
865
866 Internal modifications
867
868 - Improved input handling.
869 - Now uses w4mclassfilter R package v0.98.3, although that version has no functional implications for this tool.
870 - Improved reference-list.
871
872 Changes in version 0.98.2
873 =========================
874
875 New features
876
877 - Added support for R-flavored regular expression pattern-matching when selecting names of sample-classes.
878 - Empty classes argument or zero-length class_column result in no samples filtered out.
879
880 Internal modifications
881
882 - Support and tests for new features.
883
884 Changes in version 0.98.1
885 =========================
886
887 First release - Wrap the w4mclassfilter R package that implements filtering of W4m data matrix, variable metadata, and sample metadata by class of sample.
888
889 New features
890
891 - Output *dataMatrix* is input dataMatrix as modified by the tool
892 - Output *sampleMetadata* is input sampleMetadata as modified by the tool
893 - Output *variableMetadata* is input variableMetadata as modified by the tool
894
895 ]]></help>
896 <citations>
897 <!-- Giacomoni_2014 W4m 2.5 -->
898 <citation type="doi">10.1093/bioinformatics/btu813</citation>
899 <!-- Guitton_2017 W4m 3.0 -->
900 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
901 <!-- Kuhl_2012 CAMERA -->
902 <citation type="doi">10.1021/ac202450g</citation>
903 <!-- Smith_2006 XCMS -->
904 <citation type="doi">10.1021/ac051437y</citation>
905 <!-- Thevenot_2015 Urinary metabolome statistics -->
906 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
907 </citations>
908 <!--
909 vim:noet:sw=2:ts=2
910 --> </tool> 822 --> </tool>