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comparison Intchecks/xml_intensity_check.xml @ 3:bdee2c2c484b draft

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author melpetera
date Fri, 08 Mar 2019 09:07:12 -0500
parents a7553caa2572
children 49c36c54e0cf
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2:a7553caa2572 3:bdee2c2c484b
1 <tool id="intens_check" name="Intensity Check" version="1.0.1"> 1 <tool id="intens_check" name="Intensity Check" version="1.2.1">
2 <description>Adding information about intensities (mean fold change and missing values) in the variable metadata table</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_4">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
10 dataMatrix_in "$dataMatrix_in" 10 dataMatrix_in "$dataMatrix_in"
11 sampleMetadata_in "$sampleMetadata_in" 11 sampleMetadata_in "$sampleMetadata_in"
12 variableMetadata_in "$variableMetadata_in" 12 variableMetadata_in "$variableMetadata_in"
13 13
14 class_col "$class_col" 14 method "${method_cond.method}"
15 15
16 type "${type_cond.type}" 16 chosen_stat "${method_cond.chosen_stat}"
17 #if $type_cond.type == "One_class" : 17
18 class1 "${type_cond.class1}" 18 #if $method_cond.method == "each_class" :
19 fold_frac "${type_cond.fold_frac}" 19 class_col "${method_cond.class_col}"
20 test_fold "${method_cond.test_fold_cond.test_fold}"
21 #if $method_cond.test_fold_cond.test_fold == "Yes" :
22 logarithm "${method_cond.test_fold_cond.logarithm}"
23 #end if
20 #end if 24 #end if
21 25
22 logarithm "$logarithm" 26 #if $method_cond.method == "one_class" :
23 27 class_col "${method_cond.class_col}"
28 class1 "${method_cond.class1}"
29 test_fold "${method_cond.test_fold_cond.test_fold}"
30 #if $method_cond.test_fold_cond.test_fold == "Yes" :
31 fold_frac "${method_cond.test_fold_cond.fold_frac}"
32 logarithm "${method_cond.test_fold_cond.logarithm}"
33 #end if
34 #end if
35
24 variableMetadata_out "$variableMetadata_out" 36 variableMetadata_out "$variableMetadata_out"
25 graphs_out "$graphs_out" 37 graphs_out "$graphs_out"
38
39
40
26 </command> 41 </command>
27 42
28 <inputs> 43 <inputs>
29 <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" />
30 <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" />
31 <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" />
32 47
33 <param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" label="Class column" help="Class column in Sample metadata" /> 48 <conditional name="method_cond">
34 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">
35 <conditional name="type_cond"> 50 <option value="no_class">Without distinction between samples </option>
36 <param name="type" type="select" label="What kind of tests do you want to perform?" display="radio" help="If you only have two classes, 'One class' could be selected to choose which class should be on the numerator/denominator."> 51 <option value="each_class">For each class of samples </option>
37 <option value="One_class">Tests between one class and the remaining samples </option> 52 <option value="one_class">Between one class and all the remaining samples </option>
38 <option value="Each_class" selected="true">Tests for each class </option> 53
39 </param> 54 </param>
40 <when value="One_class"> 55
41 <param name="class1" type="text" label="Selected class" help="Class name if you choose to test one class against the remaining samples." /> 56 <when value="no_class">
42 <param name="fold_frac" type="select" label="Where should the class be placed for the mean fold change calculation?" display="radio"> 57 <param name="chosen_stat" type="select" display="checkboxes" multiple="True" label="Statistics">
43 <option value="Top">Numerator (Top) </option> 58 <option value="mean">Mean</option>
44 <option value="Bottom">Denominator (Bottom) </option> 59 <option value="sd">Standard deviation</option>
60 <option value="median">Median</option>
61 <option value="quartile">Quartile</option>
62 <option value="decile">Decile</option>
63 <option value="NA">Missing values</option>
64 <validator type="no_options" message="Please choose at least one statistic representation" />
45 </param> 65 </param>
46 </when> 66 </when>
47 <when value="Each_class"> 67
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" />
70 <param name="chosen_stat" type="select" display="checkboxes" multiple="True" label="Statistics">
71 <option value="mean">Mean</option>
72 <option value="sd">Standard deviation</option>
73 <option value="median">Median</option>
74 <option value="quartile">Quartile</option>
75 <option value="decile">Decile</option>
76 <option value="NA">Missing values</option>
77 </param>
78 <conditional name="test_fold_cond">
79 <param name="test_fold" type="select" display="radio" label="Calculate the mean fold change">
80 <option value="Yes">Yes</option>
81 <option value="No">No</option>
82 </param>
83 <when value="Yes">
84 <param name="logarithm" type="select" label="Logarithm" help="Choose if you want the mean fold change to be converted into a log mean fold change (log2 or log10)">
85 <option value="none">none </option>
86 <option value="log2">log2 </option>
87 <option value="log10">log10 </option>
88 </param>
89 </when>
90 </conditional>
91 </when>
92
93 <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" />
95 <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">
97 <option value="mean">Mean</option>
98 <option value="sd">Standard deviation</option>
99 <option value="median">Median</option>
100 <option value="quartile">Quartile</option>
101 <option value="decile">Decile</option>
102 <option value="NA">Missing values</option>
103 </param>
104 <conditional name="test_fold_cond">
105 <param name="test_fold" type="select" display="radio" label="Calculate the mean fold change">
106 <option value="Yes">Yes</option>
107 <option value="No">No</option>
108 </param>
109 <when value="Yes">
110 <param name="fold_frac" type="select" label="Where should the class be placed for the mean fold change calculation?" display="radio">
111 <option value="Top">Numerator (Top) </option>
112 <option value="Bottom">Denominator (Bottom) </option>
113 </param>
114 <param name="logarithm" type="select" label="Logarithm" help="Choose if you want the mean fold change to be converted into a log mean fold change (log2 or log10)">
115 <option value="none">none </option>
116 <option value="log2">log2 </option>
117 <option value="log10">log10 </option>
118 </param>
119 </when>
120 </conditional>
48 </when> 121 </when>
49 </conditional> 122 </conditional>
50
51 <param name="logarithm" type="select" label="Logarithm" help="Choose if you want the mean fold change to be converted into a log mean fold change (log2 or log10)">
52 <option value="none">none </option>
53 <option value="log2">log2 </option>
54 <option value="log10">log10 </option>
55 </param>
56
57 </inputs> 123 </inputs>
124
58 125
59 <outputs> 126 <outputs>
60 <data name="variableMetadata_out" label="IC_${variableMetadata_in.name}" format="tabular" /> 127 <data name="variableMetadata_out" label="IC_${variableMetadata_in.name}" format="tabular" />
61 <data name="graphs_out" label="IC_Graphs" format="pdf" /> 128 <data name="graphs_out" label="IC_Graphs" format="pdf" />
62 </outputs> 129 </outputs>
73 ======================== 140 ========================
74 Intensity Check 141 Intensity Check
75 ======================== 142 ========================
76 143
77 ----------- 144 -----------
78 Description
79 -----------
80
81 This tool performs two tests: a mean fold change calculation and the number of missing values.
82
83 **Fold:**
84 The test calculates the mean fold change between two classes. It could be converted into logarithm.
85
86 **Missing values:**
87 This tool calculates the number and the proportion of missing values in the data matrix considering the class.
88 Missing values in numerical columns of data must be coded NA.
89
90 **Two types of tests:**
91 | - Between **one class** and the remaining samples: if you have only two classes or if you want to test only one class versus all the remaining samples without class distinction.
92 | - **Each class**: if the class columns contains at least three classes and you want to test each of them. Can also be used with only two classes, but you will not choose which class to put as numerator/denominator.
93
94 -----------
95 Input files 145 Input files
96 ----------- 146 -----------
97 147
98 +----------------------------+------------+ 148 +----------------------------+------------+
99 | Parameter | Format | 149 | Parameter | Format |
107 157
108 ---------- 158 ----------
109 Parameters 159 Parameters
110 ---------- 160 ----------
111 161
162 **Computation method**
163 | - **Without distinction between samples:** calculates chosen statistic(s) for each variable.
164 | - **For each class of samples:** separates samples between each class (class column to specified). Chosen statistic(s) and/or mean fold change are calculated for each of them.
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.
166
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).
168
169 **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).
171
112 **Class column** 172 **Class column**
113 | Select the class column in sample metadata table. 173 | Select the class column in sample metadata table.
114 174
115 **Type of test**
116 | Two options:
117 | - "One class" allows to perform tests on one class against the remaining samples.
118 | - "Each class" allows to add several columns with the ratio between all the classes and the number of missing values for each class.
119
120 **Selected class** 175 **Selected class**
121 | If the type is "one class", specify it to calculate the ratio and the number of missing values. 176 | If the method is "one class", specify it. Remaining samples will be named "Other".
122 177
123 **Numerator or denominator** 178 **Calculate the mean fold change**
124 | If the type is "one class", choose "top" or "bottom" to put the selected class as numerator or denominator (respectively) for the mean fold change. 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.
180
181 **Where should the class be placed for the mean fold change calculation?**
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.
125 183
126 **Logarithm** 184 **Logarithm**
127 | Choose if you want to transform the mean fold change with a log2 or log10. 185 | Choose if you want to transform the mean fold change with a log2 or log10.
128 186
129 ------------ 187 ------------
130 Output file 188 Output file
131 ------------ 189 ------------
132 190
133 **Variable metadata file** 191 **Variable metadata file**
134 | Contains the previous columns in variable metadata file and the new ones with fold tests, number and proportion of missing values. 192 | Contains the previous columns in variable metadata file and the new ones.
135 | In the column names for fold, the first class specified is the one used like numerator for the ratio. 193 | In the column names for fold, the first class specified is the one used like numerator for the ratio.
136 194
137 **Graphs file** 195 **Graphs file**
138 | Contains barplots with the proportion of NA considering classes and boxplots with the fold values. 196 | Contains barplots with the proportion of NA considering classes and boxplots with the fold values.
139 197