annotate abims_anova.xml @ 0:8dd2a438bfba draft

Uploaded

1 <tool id="abims_anova" name="Anova" version="1.1">
2 	
3     <requirements>
4 	<requirement type="binary">Rscript</requirement>
5 	<requirement type="binary">batch</requirement>
6     </requirements>
7     
8     <description>N-way anova. With ou Without interactions</description>
9 
10     <command interpreter="Rscript">
11         abims_anova.r file "$input" sampleinfo "$sampleinfo" mode "$mode" 
12 condition "c('$condition_1'
13 #for $i, $s in enumerate( $conditions )
14 ,'${s.condition}'
15 #end for
16 )"
17 interaction $interaction method $method threshold $threshold selection_method $selection_method sep "$sep" dec "$dec" outputdatapvalue $dataMatrixPValue outputdatafiltered $dataMatrixFiltered
18     </command> 
19 
20     <inputs>
21         <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
22         <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" />
23         
24          <param name="mode" type="select" help="Perform the anova tests on column/row" format="text" optional="true">
25 		<label>Mode</label>
26 		<option value="row">row</option>
27 		<option value="column">column</option>
28 	</param>
29 	
30 	<param name="condition_1" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" optional="false" />
31 	<repeat name="conditions" title="Conditions for N-ways anova">
32 	    <param name="condition" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" />
33 	</repeat>
34 
35 	<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)" />
36         
37 	<param name="method" type="select" help="Method used to apply a correction on the pvalue because of the number of test" format="text" optional="true">
38 		<label>PValue adjusted method</label>
39 		<option value="BH">BH</option>
40 		<option value="holm">holm</option>
41 		<option value="bonferroni">bonferroni</option>
42 		<option value="hochberg">hochberg</option>
43 		<option value="hommel">hommel</option>
44 		<option value="BY">BY</option>
45 		<option value="fdr">fdr</option>
46 		<option value="none">none</option>		
47 	</param>        
48         
49         <param name="threshold" type="float" label="Threshold" value="0.01" help="max adjusted p.value accepted" />
50 
51         <param name="selection_method" type="select" format="text" help="Intersection: all condition p-value must be under the threshold. Union: at least condition p-value must be under the threshold. ">
52 		<label>Selection method</label>
53 		<option value="intersection" selected="true">intersection / strong</option>
54 		<option value="union">union / weak</option>
55 	</param>
56 
57         <param name="sep" type="select" format="text">
58 		<label>Separator of columns</label>
59 		<option value="tabulation">tabulation</option>
60 		<option value="semicolon">;</option>
61 		<option value="comma">,</option>
62 	</param>
63         
64         <param name="dec" type="text" label="Decimal separator" value="." help="" />
65 
66     </inputs>
67 
68     <outputs>
69         <data name="dataMatrixPValue" format="input" label="${input.name}_anova_pvalue.${input.ext}"/>
70         <data name="dataMatrixFiltered" format="input" label="${input.name}_anova_filtered.${input.ext}"/>
71     </outputs>
72 
73     <stdio>
74         <exit_code range="1:" level="fatal" />
75     </stdio>
76 
77     <help>
78 
79 .. class:: infomark
80 
81 **Authors** Gildas Le Corguille  ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr 
82 
83 ---------------------------------------------------
84 
85 =====
86 Anova
87 =====
88 
89 -----------
90 Description
91 -----------
92 
93 Analysis of variance (ANOVA) is used to analyze the differences between group means and their associated procedures,
94 in which the observed variance in a particular variable is partitioned into components attributable to different sources of variation.
95 
96 
97 
98 -----------
99 Input files
00 -----------
01 
02 +---------------------------+------------+
03 | Parameter : num + label   |   Format   |
04 +===========================+============+
05 | 1 : Data Matrix file      | Tabular    |
06 +---------------------------+------------+
07 | 2 : Sample Metadata file  | Tabular    |
08 +---------------------------+------------+
09 
10 
11 
12 ------------
13 Output files
14 ------------
15 
16 
17 
18 ***.anova_pvalue.tabular**
19 
20 	| A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column) + two columns (aovPValue and aovAdjPValue).
21 
22 ***.anova_filtered.tabular**
23 
24 	| The tabular file xset.anova_pvalue.tabular containing only the metabolites that have been filtered by aovAdjPValue.
25 	
26 	
27 ------
28 
29 .. class:: infomark 
30 
31 The outputs ***.anova_filtered.tabular** or ***.anova_pvalue.tabular** are tabular files. You can continue your analysis using it in the following tools:
32 	| PCA
33 	| Hierarchical Clustering
34 
35 	
36 	
37 ---------------------------------------------------
38 
39 ---------------
40 Working example
41 ---------------
42 
43 
44 Input files
45 -----------
46 
47 **>A part of an example of Data Matrix file input**
48 	
49 
50 +--------+------------------+----------------+
51 | Name   | Bur-eH_FSP_12    | Bur-eH_FSP_24  |	                                       
52 +========+==================+================+
53 |M202T601| 91206595.7559783 |106808979.08546 |
54 +--------+------------------+----------------+
55 |M234T851| 27249137.275504  |28824971.3177926|  
56 +--------+------------------+----------------+       
57 
58 **>A part of an example of Sample Metadata file input**
59 	
60 	
61 +---------------------------+------------+------------+------------+
62 | Sample name               |   class    |   time     |   batch    |
63 +===========================+============+============+============+
64 | Bur-eH_FSP_12             | Bur-eH     |    12      |     1      |
65 +---------------------------+------------+------------+------------+
66 | Bur-eH_FSP_24             | Bur-eH     |    24      |     1      |
67 +---------------------------+------------+------------+------------+
68 | Bur-NI_FSP_12             | Bur-NI     |    12      |     2      |
69 +---------------------------+------------+------------+------------+
70 | Bur-NI_FSP_24             | Bur-NI     |    24      |     2      |
71 +---------------------------+------------+------------+------------+
72 
73 Parameters
74 ----------
75 
76 	| Mode -> **row**
77 	| column name of condition -> **class**
78 	| Separator of columns: -> **tabulation**
79 	| Decimal separator -> **.**
80 	| PValue adjusted method -> **BH**
81 	| Threshold -> **0.001**
82 	
83 
84 
85 Output files
86 ------------
87 
88 **Part of an example of xset.anova_filtered.tabular:**
89 
90 .. image:: anova_pvalue.png
91 
92 **Part of an example of xset.anova_pvalue.tabular:**
93 
94 .. image:: anova_filtered.png
95 
96 
97     </help>
98 
99 </tool>