Mercurial > repos > lecorguille > anova

annotate abims_anova.xml @ 8:a2b19a78306a draft default tip

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 493595bdd63ff88e7b93f22d8a092a70d4f39a05
author lecorguille
date Mon, 05 Mar 2018 09:24:51 -0500
parents 8190dfb5a351
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
a2b19a78306a planemo upload for repository https://github.com/workflow4metabolomics/anova commit 493595bdd63ff88e7b93f22d8a092a70d4f39a05
lecorguille
parents: 7
diff changeset
1 <tool id="abims_anova" name="Anova" version="1.2.1">
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
2
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
3 <description>N-way anova. With ou Without interactions</description>
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
4
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
5 <requirements>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
6 <requirement type="package" version="1.1_4">r-batch</requirement>
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
7 <requirement type="package" version="1.2">r-venn</requirement>
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
8 </requirements>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
9
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
10 <stdio>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
11 <exit_code range="1:" level="fatal" />
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
12 </stdio>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
13
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
14 <command>
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
15 Rscript $__tool_directory__/abims_anova.r file '$input' sampleinfo '$sampleinfo' varinfo '$varinfo' mode '$mode'
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
16 condition "c('$condition_1'
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
17 #for $i, $s in enumerate( $conditions )
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
18 ,'${s.condition}'
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
19 #end for
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
20 )"
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
21 interaction $interaction
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
22 method $method
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
23 threshold $threshold
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
24 selection_method $selection_method
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
25 sep '$sep'
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
26 dec '$dec'
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
27 outputdatapvalue '$varMetaPValue'
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
28 outputdatasignif '$dataSignif'
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
29 </command>
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
30
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
31 <inputs>
8
a2b19a78306a planemo upload for repository https://github.com/workflow4metabolomics/anova commit 493595bdd63ff88e7b93f22d8a092a70d4f39a05
lecorguille
parents: 7
diff changeset
32 <param name="input" type="data" label="Data Matrix file" format="tabular,csv" help="Matrix of numeric data with headers." />
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
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" />
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
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." />
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
35
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
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">
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
37 <label>Mode</label>
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
38 <option value="row" selected="True">row</option>
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
39 <option value="column">column</option>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
40 </param>
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
41
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
42 <param name="condition_1" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" optional="false" />
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
43 <repeat name="conditions" title="Conditions for N-ways anova">
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
44 <param name="condition" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" />
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
45 </repeat>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
46
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
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)" />
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
48
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
49 <param name="method" type="select" help="Method used to apply a correction on the pvalue because of the number of test" >
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
50 <label>PValue adjusted method</label>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
51 <option value="BH">BH</option>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
52 <option value="holm">holm</option>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
53 <option value="bonferroni">bonferroni</option>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
54 <option value="hochberg">hochberg</option>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
55 <option value="hommel">hommel</option>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
56 <option value="BY">BY</option>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
57 <option value="fdr">fdr</option>
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
58 <option value="none" selected="True">none</option>
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
59 </param>
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
60
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
61 <param name="threshold" type="float" label="Threshold" value="0.01" help="max adjusted p.value accepted" />
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
62
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
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. ">
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
64 <label>Selection method</label>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
65 <option value="intersection" selected="true">intersection / strong</option>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
66 <option value="union">union / weak</option>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
67 </param>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
68
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
69 <param name="sep" type="select" format="text">
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
70 <label>Separator of columns</label>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
71 <option value="tabulation">tabulation</option>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
72 <option value="semicolon">;</option>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
73 <option value="comma">,</option>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
74 </param>
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
75
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
76 <param name="dec" type="text" label="Decimal separator" value="." help="" />
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
77
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
78 </inputs>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
79
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
80 <outputs>
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
81 <data name="varMetaPValue" format_source="varinfo" label="${varinfo.name}_anova_pvalue.${varinfo.ext}"/>
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
82 <data name="dataSignif" format="pdf" label="${input.name}_anova_signif"/>
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
83 </outputs>
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
84
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
85 <tests>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
86 <test>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
87 <param name="input" value="dataMatrix.tsv"/>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
88 <param name="sampleinfo" value="sampleMetadata.tsv"/>
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
89 <param name="varinfo" value="variableMetadata.tsv"/>
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
90 <param name="mode" value="row"/>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
91 <param name="condition_1" value="age"/>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
92 <param name="conditions_0|condition" value="gender"/>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
93 <param name="interaction" value="F"/>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
94 <param name="method" value="BH"/>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
95 <param name="threshold" value="0.05"/>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
96 <param name="selection_method" value="union"/>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
97 <param name="sep" value="tabulation"/>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
98 <param name="dev" value="."/>
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
99 <output name="varMetaPValue" file="variableMetadata.tsv_anova_pvalue.tabular" />
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
100 <output name="dataSignif" file="dataMatrix.tsv_anova_signif.pdf" compare="sim_size" delta="600" />
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
101 </test>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
102 </tests>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
103
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
104 <help>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
105
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
106 .. class:: infomark
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
107
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
108 **Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
109 Melanie Petera - PFEM ; INRA ; MetaboHUB
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
110
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
111 ---------------------------------------------------
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
112
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
113 =====
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
114 Anova
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
115 =====
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
116
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
117 -----------
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
118 Description
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
119 -----------
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
120
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
121 Analysis of variance (ANOVA) is used to analyze the differences between group means and their associated procedures,
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
122 in which the observed variance in a particular variable is partitioned into components attributable to different sources of variation.
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
123
8
a2b19a78306a planemo upload for repository https://github.com/workflow4metabolomics/anova commit 493595bdd63ff88e7b93f22d8a092a70d4f39a05
lecorguille
parents: 7
diff changeset
124 **Note about sum of squares (SS) calculation of N-way ANOVA in this module.**
a2b19a78306a planemo upload for repository https://github.com/workflow4metabolomics/anova commit 493595bdd63ff88e7b93f22d8a092a70d4f39a05
lecorguille
parents: 7
diff changeset
125 This module use R function *manova()* (and thus R function *aov()*) to establish N-way ANOVA.
a2b19a78306a planemo upload for repository https://github.com/workflow4metabolomics/anova commit 493595bdd63ff88e7b93f22d8a092a70d4f39a05
lecorguille
parents: 7
diff changeset
126 Therefore calculated sum of squares are sequential ones (sometimes called "Type I SS").
a2b19a78306a planemo upload for repository https://github.com/workflow4metabolomics/anova commit 493595bdd63ff88e7b93f22d8a092a70d4f39a05
lecorguille
parents: 7
diff changeset
127 If your design is unbalanced, this may not correspond to the type of hypothesis being of interest.
a2b19a78306a planemo upload for repository https://github.com/workflow4metabolomics/anova commit 493595bdd63ff88e7b93f22d8a092a70d4f39a05
lecorguille
parents: 7
diff changeset
128 Note that you can obtain adjusted sums of squares ("Type II SS") by running several times this module with different orders in factors.
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
129
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
130
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
131 -----------
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
132 Input files
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
133 -----------
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
134
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
135 +----------------------------+------------+
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
136 | Parameter : num + label | Format |
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
137 +============================+============+
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
138 | 1 : Data Matrix file | Tabular |
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
139 +----------------------------+------------+
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
140 | 2 : Sample Metadata file | Tabular |
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
141 +----------------------------+------------+
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
142 | 3 : Variable Metadata file | Tabular |
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
143 +----------------------------+------------+
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
144
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
145
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
146 ------------
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
147 Output files
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
148 ------------
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
149
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
150
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
151
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
152 ***.anova_pvalue.tabular**
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
153
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
154 | Your variable metadata file completed with columns of p-values, result of selection method and means of subgroups.
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
155
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
156 ***.anova_signif.pdf**
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
157
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
158 | A pdf file containing a Venn diagram and boxplots of significant variables.
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
159
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
160
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
161 ------
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
162
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
163 .. class:: infomark
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
164
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
165 The outputs ***.anova_filtered.tabular** is a tabular file. You can continue your analysis using it in the following tools:
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
166
7
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
167 | Generic_filter
8190dfb5a351 planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
lecorguille
parents: 6
diff changeset
168 | Hierarchical Clustering
6
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
169
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
170
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
171
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
172 ---------------------------------------------------
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
173
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
174
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
175
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
176 </help>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
177
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
178 <citations>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
179 <citation type="bibtex">@ARTICLE{fisher,
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
180 author = {Ronald A. Fisher},
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
181 title = {The Correlation between Relatives on the Supposition of Mendelian Inheritance},
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
182 journal = {Philosophical Transactions of the Royal Society of Edinburgh},
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
183 year = {1918},
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
184 volume = {52},
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
185 pages = {399-433}
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
186 }</citation>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
187 </citations>
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
188
0f8a79085317 planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
lecorguille
parents:
diff changeset
189 </tool>