Mercurial > repos > lecorguille > anova

comparison abims_anova.xml @ 10:b147b17759a6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
author lecorguille
date Wed, 28 Feb 2018 07:44:13 -0500
parents 4f06e1796334
children 102049093b7d
comparison
equal deleted inserted replaced
9:4f06e1796334 10:b147b17759a6
1 <tool id="abims_anova" name="Anova" version="1.1.4"> 1 <tool id="abims_anova" name="Anova" version="1.2.0">
2 2
3 <description>N-way anova. With ou Without interactions</description> 3 <description>N-way anova. With ou Without interactions</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1.1_4">r-batch</requirement> 6 <requirement type="package" version="1.1_4">r-batch</requirement>
7 <requirement type="package" version="1.2">r-venn</requirement>
7 </requirements> 8 </requirements>
8 9
9 <stdio> 10 <stdio>
10 <exit_code range="1:" level="fatal" /> 11 <exit_code range="1:" level="fatal" />
11 </stdio> 12 </stdio>
12 13
13 <command> 14 <command>
14 Rscript $__tool_directory__/abims_anova.r file '$input' sampleinfo '$sampleinfo' mode '$mode' 15 Rscript $__tool_directory__/abims_anova.r file '$input' sampleinfo '$sampleinfo' varinfo '$varinfo' mode '$mode'
15 condition "c('$condition_1' 16 condition "c('$condition_1'
16 #for $i, $s in enumerate( $conditions ) 17 #for $i, $s in enumerate( $conditions )
17 ,'${s.condition}' 18 ,'${s.condition}'
18 #end for 19 #end for
19 )" 20 )"
20 interaction $interaction 21 interaction $interaction
21 method $method 22 method $method
22 threshold $threshold 23 threshold $threshold
23 selection_method $selection_method 24 selection_method $selection_method
24 sep '$sep' 25 sep '$sep'
25 dec '$dec' 26 dec '$dec'
26 outputdatapvalue '$dataMatrixPValue' 27 outputdatapvalue '$varMetaPValue'
27 outputdatafiltered '$dataMatrixFiltered' 28 outputdatasignif '$dataSignif'
28 </command> 29 </command>
29 30
30 <inputs> 31 <inputs>
31 <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." /> 32 <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
32 <param name="sampleinfo" type="data" label="Sample Metadata file" format="tabular" help="Tabular file with the data metadata : one sample per line and at least two columns : ids and one condition" /> 33 <param name="sampleinfo" type="data" label="Sample Metadata file" format="tabular" help="Tabular file with the data metadata : one sample per line and at least two columns : ids and one condition" />
33 34 <param name="varinfo" type="data" label="Variable Metadata file" format="tabular" help="Tabular file with information about your tested variables. Only used to aggregate generated information." />
34 <param name="mode" type="select" help="Perform the anova tests on column/row" format="text" optional="true"> 35
36 <param name="mode" type="select" help="Perform the anova tests on column/row; for W4M 3-tables format, use 'row'." format="text" optional="true">
35 <label>Mode</label> 37 <label>Mode</label>
36 <option value="row">row</option> 38 <option value="row" selected="True">row</option>
37 <option value="column">column</option> 39 <option value="column">column</option>
38 </param> 40 </param>
39 41
40 <param name="condition_1" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" optional="false" /> 42 <param name="condition_1" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" optional="false" />
41 <repeat name="conditions" title="Conditions for N-ways anova"> 43 <repeat name="conditions" title="Conditions for N-ways anova">
42 <param name="condition" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" /> 44 <param name="condition" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" />
43 </repeat> 45 </repeat>
44 46
45 <param name="interaction" type="boolean" label="Enable interaction response p-values" truevalue="T" falsevalue="F" help="Used if more than 1 conditon. The anova will produse p-value according to the interaction between your condition (ex: condition1:conditions2, condition1:conditions3, condition2:conditions3 and condition1:condition2:conditions3)" /> 47 <param name="interaction" type="boolean" label="Enable interaction response p-values" truevalue="T" falsevalue="F" help="Used if more than 1 conditon. The anova will produse p-value according to the interaction between your condition (ex: condition1:conditions2, condition1:conditions3, condition2:conditions3 and condition1:condition2:conditions3)" />
46 48
47 <param name="method" type="select" help="Method used to apply a correction on the pvalue because of the number of test" > 49 <param name="method" type="select" help="Method used to apply a correction on the pvalue because of the number of test" >
48 <label>PValue adjusted method</label> 50 <label>PValue adjusted method</label>
49 <option value="BH">BH</option> 51 <option value="BH">BH</option>
50 <option value="holm">holm</option> 52 <option value="holm">holm</option>
51 <option value="bonferroni">bonferroni</option> 53 <option value="bonferroni">bonferroni</option>
52 <option value="hochberg">hochberg</option> 54 <option value="hochberg">hochberg</option>
53 <option value="hommel">hommel</option> 55 <option value="hommel">hommel</option>
54 <option value="BY">BY</option> 56 <option value="BY">BY</option>
55 <option value="fdr">fdr</option> 57 <option value="fdr">fdr</option>
56 <option value="none">none</option> 58 <option value="none" selected="True">none</option>
57 </param> 59 </param>
58 60
59 <param name="threshold" type="float" label="Threshold" value="0.01" help="max adjusted p.value accepted" /> 61 <param name="threshold" type="float" label="Threshold" value="0.01" help="max adjusted p.value accepted" />
60 62
61 <param name="selection_method" type="select" help="Intersection: all condition p-value must be under the threshold. Union: at least condition p-value must be under the threshold. "> 63 <param name="selection_method" type="select" help="Intersection: all condition p-value must be under the threshold. Union: at least condition p-value must be under the threshold. ">
62 <label>Selection method</label> 64 <label>Selection method</label>
63 <option value="intersection" selected="true">intersection / strong</option> 65 <option value="intersection" selected="true">intersection / strong</option>
68 <label>Separator of columns</label> 70 <label>Separator of columns</label>
69 <option value="tabulation">tabulation</option> 71 <option value="tabulation">tabulation</option>
70 <option value="semicolon">;</option> 72 <option value="semicolon">;</option>
71 <option value="comma">,</option> 73 <option value="comma">,</option>
72 </param> 74 </param>
73 75
74 <param name="dec" type="text" label="Decimal separator" value="." help="" /> 76 <param name="dec" type="text" label="Decimal separator" value="." help="" />
75 77
76 </inputs> 78 </inputs>
77 79
78 <outputs> 80 <outputs>
79 <data name="dataMatrixPValue" format_source="input" label="${input.name}_anova_pvalue.${input.ext}"/> 81 <data name="varMetaPValue" format_source="varinfo" label="${varinfo.name}_anova_pvalue.${varinfo.ext}"/>
80 <data name="dataMatrixFiltered" format_source="input" label="${input.name}_anova_filtered.${input.ext}"/> 82 <data name="dataSignif" format="pdf" label="${input.name}_anova_signif"/>
81 </outputs> 83 </outputs>
82 84
83 <tests> 85 <tests>
84 <test> 86 <test>
85 <param name="input" value="dataMatrix.tsv"/> 87 <param name="input" value="dataMatrix.tsv"/>
86 <param name="sampleinfo" value="sampleMetadata.tsv"/> 88 <param name="sampleinfo" value="sampleMetadata.tsv"/>
89 <param name="varinfo" value="variableMetadata.tsv"/>
87 <param name="mode" value="row"/> 90 <param name="mode" value="row"/>
88 <param name="condition_1" value="age"/> 91 <param name="condition_1" value="age"/>
89 <param name="conditions_0|condition" value="gender"/> 92 <param name="conditions_0|condition" value="gender"/>
90 <param name="interaction" value="F"/> 93 <param name="interaction" value="F"/>
91 <param name="method" value="BH"/> 94 <param name="method" value="BH"/>
92 <param name="threshold" value="0.05"/> 95 <param name="threshold" value="0.05"/>
93 <param name="selection_method" value="union"/> 96 <param name="selection_method" value="union"/>
94 <param name="sep" value="tabulation"/> 97 <param name="sep" value="tabulation"/>
95 <param name="dev" value="."/> 98 <param name="dev" value="."/>
96 <output name="dataMatrixPValue" file="dataMatrix.tsv_anova_pvalue.tabular" /> 99 <output name="varMetaPValue" file="variableMetadata.tsv_anova_pvalue.tabular" />
97 <output name="dataMatrixFiltered" file="dataMatrix.tsv_anova_filtered.tabular" /> 100 <output name="dataSignif" file="dataMatrix.tsv_anova_signif.pdf" compare="sim_size" delta="600" />
98 </test> 101 </test>
99 </tests> 102 </tests>
100 103
101 <help> 104 <help>
102 105
103 .. class:: infomark 106 .. class:: infomark
104 107
105 **Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr 108 **Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr
109 Melanie Petera - PFEM ; INRA ; MetaboHUB
106 110
107 --------------------------------------------------- 111 ---------------------------------------------------
108 112
109 ===== 113 =====
110 Anova 114 Anova
121 125
122 ----------- 126 -----------
123 Input files 127 Input files
124 ----------- 128 -----------
125 129
126 +---------------------------+------------+ 130 +----------------------------+------------+
127 | Parameter : num + label | Format | 131 | Parameter : num + label | Format |
128 +===========================+============+ 132 +============================+============+
129 | 1 : Data Matrix file | Tabular | 133 | 1 : Data Matrix file | Tabular |
130 +---------------------------+------------+ 134 +----------------------------+------------+
131 | 2 : Sample Metadata file | Tabular | 135 | 2 : Sample Metadata file | Tabular |
132 +---------------------------+------------+ 136 +----------------------------+------------+
133 137 | 3 : Variable Metadata file | Tabular |
138 +----------------------------+------------+
134 139
135 140
136 ------------ 141 ------------
137 Output files 142 Output files
138 ------------ 143 ------------
139 144
140 145
141 146
142 ***.anova_pvalue.tabular** 147 ***.anova_pvalue.tabular**
143 148
144 | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column) + two columns (aovPValue and aovAdjPValue). 149 | Your variable metadata file completed with columns of p-values, result of selection method and means of subgroups.
145 150
146 ***.anova_filtered.tabular** 151 ***.anova_signif.pdf**
147 152
148 | The tabular file xset.anova_pvalue.tabular containing only the metabolites that have been filtered by aovAdjPValue. 153 | A pdf file containing a Venn diagram and boxplots of significant variables.
149 154
150 155
151 ------ 156 ------
152 157
153 .. class:: infomark 158 .. class:: infomark
154 159
155 The outputs ***.anova_filtered.tabular** or ***.anova_pvalue.tabular** are tabular files. You can continue your analysis using it in the following tools: 160 The outputs ***.anova_filtered.tabular** is a tabular file. You can continue your analysis using it in the following tools:
156 161
157 | PCA 162 | Generic_filter
158 | Hierarchical Clustering 163 | Hierarchical Clustering
159 164
160
161
162 ---------------------------------------------------
163
164 ---------------
165 Working example
166 ---------------
167
168
169 Input files
170 -----------
171
172 **>A part of an example of Data Matrix file input**
173
174
175 +--------+------------------+----------------+
176 | Name | Bur-eH_FSP_12 | Bur-eH_FSP_24 |
177 +========+==================+================+
178 |M202T601| 91206595.7559783 |106808979.08546 |
179 +--------+------------------+----------------+
180 |M234T851| 27249137.275504 |28824971.3177926|
181 +--------+------------------+----------------+
182
183 **>A part of an example of Sample Metadata file input**
184
185
186 +---------------------------+------------+------------+------------+
187 | Sample name | class | time | batch |
188 +===========================+============+============+============+
189 | Bur-eH_FSP_12 | Bur-eH | 12 | 1 |
190 +---------------------------+------------+------------+------------+
191 | Bur-eH_FSP_24 | Bur-eH | 24 | 1 |
192 +---------------------------+------------+------------+------------+
193 | Bur-NI_FSP_12 | Bur-NI | 12 | 2 |
194 +---------------------------+------------+------------+------------+
195 | Bur-NI_FSP_24 | Bur-NI | 24 | 2 |
196 +---------------------------+------------+------------+------------+
197
198 Parameters
199 ----------
200
201 | Mode -> **row**
202 | column name of condition -> **class**
203 | Separator of columns: -> **tabulation**
204 | Decimal separator -> **.**
205 | PValue adjusted method -> **BH**
206 | Threshold -> **0.001**
207
208
209
210 Output files
211 ------------
212
213 **Part of an example of xset.anova_filtered.tabular:**
214
215 .. image:: anova_pvalue.png
216
217 **Part of an example of xset.anova_pvalue.tabular:**
218
219 .. image:: anova_filtered.png
220 165
221 166
222 --------------------------------------------------- 167 ---------------------------------------------------
223 168
224
225 ---------------------------
226 Position in workflow4metabo
227 ---------------------------
228 169
229
230 **Upstream tools**
231
232 +---------------------------+----------------------------------------+--------+------------------------+
233 | Name | Output file | Format | parameter |
234 +===========================+========================================+========+========================+
235 |CAMERA.annotateDiffreport |xset.annotatediffreport.data_matrix.tsv | Tabular| Data table file |
236 +---------------------------+----------------------------------------+--------+------------------------+
237 |xcms.xcmsSet |sample_info.tab | Tabular| sample info table file |
238 +---------------------------+----------------------------------------+--------+------------------------+
239
240
241 **Downstream tools**
242
243 +---------------------------+---------------------------------------------------------+--------+
244 | Name | Output file | Format |
245 +===========================+=========================================================+========+
246 |PCA |xset.anova_pvalue.tabular OR xset.anova_filtered.tabular | Tabular|
247 +---------------------------+---------------------------------------------------------+--------+
248 |Hierarchical Clustering |xset.anova_pvalue.tabular OR xset.anova_filtered.tabular | Tabular|
249 +---------------------------+---------------------------------------------------------+--------+
250
251
252 **General schema of the metabolomic workflow**
253
254 .. image:: anova_workflow.png
255 170
256 </help> 171 </help>
257 172
258 <citations> 173 <citations>
259 <citation type="bibtex">@ARTICLE{fisher, 174 <citation type="bibtex">@ARTICLE{fisher,