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comparison Intchecks/xml_intensity_check.xml @ 6:ec75de7f1e08 draft default tip

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author melpetera
date Mon, 11 Dec 2023 12:56:20 +0000
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5:a31f3f802b2b 6:ec75de7f1e08
1 <tool id="intens_check" name="Intensity Check" version="1.2.8"> 1 <tool id="intens_check" name="Intensity Check" version="1.3.0">
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="4.2.1">r-base</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
64 <validator type="no_options" message="Please choose at least one statistic representation" /> 64 <validator type="no_options" message="Please choose at least one statistic representation" />
65 </param> 65 </param>
66 </when> 66 </when>
67 67
68 <when value="each_class"> 68 <when value="each_class">
69 <param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" label="Class column" help="Class column in Sample metadata" /> 69 <param name="class_col" type="text" label="Class column" help="Name of the column in Sample metadata" />
70 <param name="chosen_stat" type="select" display="checkboxes" multiple="True" label="Statistics"> 70 <param name="chosen_stat" type="select" display="checkboxes" multiple="True" label="Statistics">
71 <option value="mean">Mean</option> 71 <option value="mean">Mean</option>
72 <option value="sd">Standard deviation</option> 72 <option value="sd">Standard deviation</option>
73 <option value="median">Median</option> 73 <option value="median">Median</option>
74 <option value="quartile">Quartile</option> 74 <option value="quartile">Quartile</option>
85 <option value="none">none </option> 85 <option value="none">none </option>
86 <option value="log2">log2 </option> 86 <option value="log2">log2 </option>
87 <option value="log10">log10 </option> 87 <option value="log10">log10 </option>
88 </param> 88 </param>
89 </when> 89 </when>
90 <when value="No">
91 </when>
90 </conditional> 92 </conditional>
91 </when> 93 </when>
92 94
93 <when value="one_class"> 95 <when value="one_class">
94 <param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" label="Class column" help="Class column in Sample metadata" /> 96 <param name="class_col" type="text" label="Class column" help="Name of the column in Sample metadata" />
95 <param name="class1" type="text" label="Selected class" help="Name of the class to test versus all the remaining samples." /> 97 <param name="class1" type="text" label="Selected class" help="Name of the class to test versus all the remaining samples." />
96 <param name="chosen_stat" type="select" display="checkboxes" multiple="True" label="Statistics"> 98 <param name="chosen_stat" type="select" display="checkboxes" multiple="True" label="Statistics">
97 <option value="mean">Mean</option> 99 <option value="mean">Mean</option>
98 <option value="sd">Standard deviation</option> 100 <option value="sd">Standard deviation</option>
99 <option value="median">Median</option> 101 <option value="median">Median</option>
115 <option value="none">none </option> 117 <option value="none">none </option>
116 <option value="log2">log2 </option> 118 <option value="log2">log2 </option>
117 <option value="log10">log10 </option> 119 <option value="log10">log10 </option>
118 </param> 120 </param>
119 </when> 121 </when>
122 <when value="No">
123 </when>
120 </conditional> 124 </conditional>
121 </when> 125 </when>
122 </conditional> 126 </conditional>
123 </inputs> 127 </inputs>
124 128
127 <data name="variableMetadata_out" label="IC_${variableMetadata_in.name}" format="tabular" /> 131 <data name="variableMetadata_out" label="IC_${variableMetadata_in.name}" format="tabular" />
128 <data name="graphs_out" label="IC_Graphs" format="pdf" /> 132 <data name="graphs_out" label="IC_Graphs" format="pdf" />
129 </outputs> 133 </outputs>
130 134
131 135
132 136 <tests>
137 <test>
138 <param name="dataMatrix_in" value="input_IC_DM.txt"/>
139 <param name="sampleMetadata_in" value="input_IC_SM.txt"/>
140 <param name="variableMetadata_in" value="input_IC_VM.txt"/>
141 <param name="method" value="one_class"/>
142 <param name="chosen_stat" value="mean,sd,NA"/>
143 <param name="class_col" value="uv"/>
144 <param name="class1" value="s"/>
145 <param name="test_fold" value="Yes"/>
146 <param name="fold_frac" value="Bottom"/>
147 <param name="logarithm" value="log2"/>
148 <output name="variableMetadata_out" file="output_IC_VM.tabular"/>
149 </test>
150 </tests>
133 151
134 <help> 152 <help>
135 153
136 .. class:: infomark 154 .. class:: infomark
137 155
192 210
193 **Statistics** 211 **Statistics**
194 | 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). 212 | 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).
195 213
196 **Class column** (*only if "each class" or "one class"*) 214 **Class column** (*only if "each class" or "one class"*)
197 | Select the class column in sample metadata table. 215 | Fill the name of the class column in sample metadata table; it is case-sensitive.
198 216
199 **Selected class** (*only if "one class"*) 217 **Selected class** (*only if "one class"*)
200 | If the method is "one class", specify it. Remaining samples will be named "Other". 218 | If the method is "one class", specify it. Remaining samples will be named "Other".
201 219
202 **Calculate the mean fold change** (*only if "each class" or "one class"*) 220 **Calculate the mean fold change** (*only if "each class" or "one class"*)
229 247
230 248
231 .. class:: warningmark 249 .. class:: warningmark
232 250
233 For more information about input files, refer to the corresponding "W4M HowTo" page: 251 For more information about input files, refer to the corresponding "W4M HowTo" page:
234 | `W4M table format for Galaxy &lt;http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf&gt;`_ 252 | `W4M table format for Galaxy &lt;https://workflow4metabolomics.org/sites/default/files/fichiers/documents/w4m_TableFormatForGalaxy_150908.pdf&gt;`_
235 | 253 |
236 254
237 255
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239 257