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comparison Intchecks/xml_intensity_check.xml @ 4:49c36c54e0cf draft

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author melpetera
date Fri, 03 Jan 2020 11:09:05 -0500
parents bdee2c2c484b
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1 <tool id="intens_check" name="Intensity Check" version="1.2.1"> 1 <tool id="intens_check" name="Intensity Check" version="1.2.8">
2 <description>Statistical measures, number of missing values and mean fold change</description> 2 <description>Statistical measures, number of missing values and mean fold change</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1_5">r-batch</requirement> 4 <requirement type="package" version="1.1_5">r-batch</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="Rscript"> 6 <command interpreter="Rscript">
7 7
8 wrapper_intensity_check.R 8 wrapper_intensity_check.R
9 9
39 39
40 40
41 </command> 41 </command>
42 42
43 <inputs> 43 <inputs>
44 <param name="dataMatrix_in" type="data" label="Data Matrix file" help="" format="tabular" /> 44 <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
45 <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" /> 45 <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
46 <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" /> 46 <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
47 47
48 <conditional name="method_cond"> 48 <conditional name="method_cond">
49 <param name="method" type="select" label="Computation method" help="Select the first method if you don't want to take into account any class of samples"> 49 <param name="method" type="select" label="Computation method" help="Select the first method if you don't want to take into account any class of samples">
126 <outputs> 126 <outputs>
127 <data name="variableMetadata_out" label="IC_${variableMetadata_in.name}" format="tabular" /> 127 <data name="variableMetadata_out" label="IC_${variableMetadata_in.name}" format="tabular" />
128 <data name="graphs_out" label="IC_Graphs" format="pdf" /> 128 <data name="graphs_out" label="IC_Graphs" format="pdf" />
129 </outputs> 129 </outputs>
130 130
131
132
131 <help> 133 <help>
132 134
133 .. class:: infomark 135 .. class:: infomark
134 136
135 **Authors** 137 **Author:**
136 | Anthony Fernandes - PFEM ; INRA 138 Anthony Fernandes for original code (PFEM - INRA)
139 **Maintainer:** Melanie Petera (PFEM - INRAE - MetaboHUB)
137 140
138 --------------------------------------------------- 141 ---------------------------------------------------
139 142
140 ======================== 143 ========================
141 Intensity Check 144 Intensity Check
142 ======================== 145 ========================
143 146
144 ----------- 147 -----------
148 Description
149 -----------
150
151 This tool performs various metrics: mean fold change calculation, number and proportion of missing values, and mean, sd and decile calculation.
152 You can choose to perform these metrics according to sample groups defined in the sample metadata file given as input.
153
154
155 -----------------
156 Workflow position
157 -----------------
158
159
160 .. image:: int_check.png
161 :width: 800
162
163
164 -----------
145 Input files 165 Input files
146 ----------- 166 -----------
147 167
148 +----------------------------+------------+ 168 +----------------------------+------------+
149 | Parameter | Format | 169 | Parameter | Format |
150 +============================+============+ 170 +============================+============+
151 | 1 : Data Matrix file | tabular | 171 | 1 : Data matrix file | tabular |
152 +----------------------------+------------+ 172 +----------------------------+------------+
153 | 2 : Sample metadata file | tabular | 173 | 2 : Sample metadata file | tabular |
154 +----------------------------+------------+ 174 +----------------------------+------------+
155 | 3 : Variable metadata file | tabular | 175 | 3 : Variable metadata file | tabular |
156 +----------------------------+------------+ 176 +----------------------------+------------+
177
178 |
179
157 180
158 ---------- 181 ----------
159 Parameters 182 Parameters
160 ---------- 183 ----------
161 184
165 | - **Between one class versus all the remaining samples:** If you want to focus only on one class versus all the remaining samples without class distinction. 188 | - **Between one class versus all the remaining samples:** If you want to focus only on one class versus all the remaining samples without class distinction.
166 189
167 | In the case of two classes: "each class" and "one class" give the same results for statistical measures. We recommend to choose "one class" for mean fold change calculation in order to select the class you want to put as numerator or denominator (see below). 190 | In the case of two classes: "each class" and "one class" give the same results for statistical measures. We recommend to choose "one class" for mean fold change calculation in order to select the class you want to put as numerator or denominator (see below).
168 191
169 **Statistics** 192 **Statistics**
170 | Select the statistical measures you want to add in the variable metadata table. If the method is "each class" or "one class", you could choose no statistical measure if you only want to calculate the mean fold change (see below). 193 | Select the statistical measures you want to add in the variable metadata table. If the method is "each class" or "one class", you can choose to leave this section blank if you only want to calculate the mean fold change (see below).
171 194
172 **Class column** 195 **Class column** (*only if "each class" or "one class"*)
173 | Select the class column in sample metadata table. 196 | Select the class column in sample metadata table.
174 197
175 **Selected class** 198 **Selected class** (*only if "one class"*)
176 | If the method is "one class", specify it. Remaining samples will be named "Other". 199 | If the method is "one class", specify it. Remaining samples will be named "Other".
177 200
178 **Calculate the mean fold change** 201 **Calculate the mean fold change** (*only if "each class" or "one class"*)
179 | Choose if you want to calculate the mean fold change. If the method is "each class": mean fold change will be calculated for all combinations of classes. If the method is "one class": it will be calculated between the selected class (see above) and the remaining samples. 202 | Choose if you want to calculate the mean fold change. If the method is "each class": mean fold change will be calculated for all combinations of classes. If the method is "one class": it will be calculated between the selected class (see above) and the remaining samples.
180 203
181 **Where should the class be placed for the mean fold change calculation?** 204 **Where should the class be placed for the mean fold change calculation?** (*only if "one class"*)
182 | If the method is "one class", choose "top" or "bottom" to put the selected class as numerator or denominator (respectively) for the mean fold change calculation. 205 | If the method is "one class", choose "top" or "bottom" to put the selected class as numerator or denominator (respectively) for the mean fold change calculation.
183 206
184 **Logarithm** 207 **Logarithm** (*only if "each class" or "one class"*)
185 | Choose if you want to transform the mean fold change with a log2 or log10. 208 | Choose if you want to transform the mean fold change with a log2 or log10.
186 209
187 ------------ 210 ------------
188 Output file 211 Output file
189 ------------ 212 ------------
190 213
191 **Variable metadata file** 214 **Variable metadata file**
192 | Contains the previous columns in variable metadata file and the new ones. 215 | Contains the previous columns in variable metadata file and the new ones.
193 | In the column names for fold, the first class specified is the one used like numerator for the ratio. 216 | In the column names for fold, the first class specified is the one used as numerator in the ratio.
194 217
195 **Graphs file** 218 **Graphs file**
196 | Contains barplots with the proportion of NA considering classes and boxplots with the fold values. 219 | Contains barplots with the proportion of NA considering classes and boxplots with the fold values.
197 220
221
222
223 ---------------------------------------------------
224
225 ----------------------
226 Additional information
227 ----------------------
228
229
230 .. class:: warningmark
231
232 For more information about input files, refer to the corresponding "W4M HowTo" page:
233 | `W4M table format for Galaxy &lt;http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf&gt;`_
234 |
235
236
237
238
239
240
198 </help> 241 </help>
199 242
200 243
201 </tool> 244 </tool>
202 245