annotate edger-repenrich2.xml @ 9:2b61c6407efb draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 961a14cd73dd8e40b2f30d5e4df136b98cd8f07a
author artbio
date Thu, 25 Apr 2024 16:22:34 +0000
parents 6d59fbca2db4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
1 <tool id="edger-repenrich2" name="edgeR-repenrich2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
2 <description>Determines differentially expressed features from RepEnrich2 counts</description>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
3 <macros>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
4 <import>macros.xml</import>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
5 </macros>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
6 <expand macro="edgeR_requirements"/>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
7 <stdio>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
8 <regex match="Execution halted"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
9 source="both"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
10 level="fatal"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
11 description="Execution halted." />
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
12 <regex match="Error in"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
13 source="both"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
14 level="fatal"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
15 description="An undefined error occurred, please check your input carefully and contact your administrator." />
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
16 <regex match="Fatal error"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
17 source="both"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
18 level="fatal"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
19 description="An undefined error occurred, please check your input carefully and contact your administrator." />
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
20 </stdio>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
21 <version_command>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
22 <![CDATA[
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
23 echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR) &&
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
24 cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
25 ]]>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
26 </version_command>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
27 <command>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
28 <![CDATA[
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
29 #import json
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
30 Rscript '${__tool_directory__}/edgeR_repenrich2.R'
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
31 --factorName '$factorName'
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
32
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
33 --levelNameA '$factorLevel_A'
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
34 #set $factorlevelsA = list()
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
35 #for $file in $countsFiles_A:
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
36 $factorlevelsA.append(str($file))
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
37 #end for
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
38 $factorlevelsA.reverse()
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
39 --levelAfiles '#echo json.dumps(factorlevelsA)#'
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
40
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
41 --levelNameB '$factorLevel_B'
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
42 #set $factorlevelsB = list()
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
43 #for $file in $countsFiles_B:
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
44 $factorlevelsB.append(str($file))
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
45 #end for
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
46 $factorlevelsB.reverse()
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
47 --levelBfiles '#echo json.dumps(factorlevelsB)#'
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
48
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
49 -o 'edger_out'
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
50
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
51 -p '$plots'
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
52 #if $normCounts:
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
53 -n '$counts_out'
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
54 #end if
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
55 -o '$edger_out'
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
56 ]]>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
57 </command>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
58 <inputs>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
59 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. genotype or age or drug_x"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
60 help="Only letters, numbers and underscores will be retained in this field">
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
61 <sanitizer>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
62 <valid initial="string.letters,string.digits"><add value="_" /></valid>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
63 </sanitizer>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
64 </param>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
65 <param name="factorLevel_A" type="text" value="FactorLevel1" label="Specify a factor level, typical values could be 'mutant' or 'Drug_X'"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
66 help="Only letters, numbers and underscores will be retained in this field">
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
67 <sanitizer>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
68 <valid initial="string.letters,string.digits"><add value="_" /></valid>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
69 </sanitizer>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
70 </param>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
71 <param name="countsFiles_A" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich" />
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
72 <param name="factorLevel_B" type="text" value="FactorLevel2" label="Specify a factor level, typical values could be 'wildtype' or 'control'"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
73 help="Only letters, numbers and underscores will be retained in this field">
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
74 <sanitizer>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
75 <valid initial="string.letters,string.digits"><add value="_" /></valid>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
76 </sanitizer>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
77 </param>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
78 <param name="countsFiles_B" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich tool" />
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
79 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
80 label="Output normalized counts table" />
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
81 </inputs>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
82 <outputs>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
83 <data format="tabular" name="edger_out" label="edgeR: ${factorLevel_A} compared to ${factorLevel_B}">
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
84 <actions>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
85 <action name="column_names" type="metadata" default="Tag,log2(FC),FDR,Class,Type" />
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
86 </actions>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
87 </data>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
88 <data format="pdf" name="plots" label="edgeR plots" />
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
89 <data format="tabular" name="counts_out" label="Normalized counts file">
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
90 <filter>normCounts == True</filter>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
91 </data>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
92 </outputs>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
93 <tests>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
94 <test expect_num_outputs="3">
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
95 <param name="factorName" value="Genotype"/>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
96 <param name="factorLevel_A" value="Mutant"/>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
97 <param name="countsFiles_A" value="355_fraction_counts.tab,356_fraction_counts.tab"/>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
98 <param name="factorLevel_B" value="Wildtype"/>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
99 <param name="countsFiles_B" value="353_fraction_counts.tab,354_fraction_counts.tab"/>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
100 <param name="normCounts" value="True"/>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
101 <output name="counts_out" file="Normalized_counts_file.tab"/>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
102 <output name="plots" file="edgeR_plots.pdf"/>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
103 <output name="edger_out" file="edgeR_result_file.tab"/>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
104
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
105 </test>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
106 </tests>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
107 <help>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
108 <![CDATA[
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
109 .. class:: infomark
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
110
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
111 **What it does**
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
112
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
113 Estimate Distance between samples (MDS) and Biological Coefficient Variation (BCV) in count
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
114 data from high-throughput sequencing assays and test for differential expression using edgeR_.
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
115
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
116 **Inputs**
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
117
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
118 edger-repenrich takes count tables generated by repenrich as inputs. A repenrich count table looks
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
119 like:
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
120
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
121 ============== ========== ========== ==========
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
122 LSU-rRNA_Dme rRNA rRNA 3659329
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
123 -------------- ---------- ---------- ----------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
124 FW3_DM LINE Jockey 831
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
125 -------------- ---------- ---------- ----------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
126 DMTOM1_LTR LTR Gypsy 1004
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
127 -------------- ---------- ---------- ----------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
128 R1_DM LINE R1 7343
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
129 -------------- ---------- ---------- ----------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
130 TAHRE LINE Jockey 4560
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
131 -------------- ---------- ---------- ----------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
132 G4_DM LINE Jockey 3668
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
133 -------------- ---------- ---------- ----------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
134 BS LINE Jockey 7296
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
135 -------------- ---------- ---------- ----------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
136 Stalker2_I-int LTR Gypsy 12252
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
137 -------------- ---------- ---------- ----------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
138 Stalker3_LTR LTR Gypsy 593
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
139 -------------- ---------- ---------- ----------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
140 TABOR_I-int LTR Gypsy 3947
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
141 -------------- ---------- ---------- ----------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
142 G7_DM LINE Jockey 162
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
143 -------------- ---------- ---------- ----------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
144 BEL_I-int LTR Pao 23757
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
145 -------------- ---------- ---------- ----------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
146 Gypsy6_I-int LTR Gypsy 7489
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
147 ============== ========== ========== ==========
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
148
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
149 Count tables must be generated for each sample individually. Here, edgeR_ is handling a
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
150 single factor (genotype, age, treatment, etc) that effect your experiment. This factor has
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
151 two levels/states (for instance, "wild-type" and "mutant". You need to select appropriate
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
152 count table from your history for each factor level.
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
153
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
154 The following table gives some examples of factors and their levels:
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
155
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
156 ========= ============== ===============
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
157 Factor Factorlevel1 Factorlevel2
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
158 --------- -------------- ---------------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
159 Treatment Treated Untreated
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
160 --------- -------------- ---------------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
161 Genotype Knockdown Wildtype
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
162 --------- -------------- ---------------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
163 TimePoint Day4 Day1
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
164 --------- -------------- ---------------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
165 Gender Female Male
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
166 ========= ============== ===============
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
167
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
168 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2.
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
169 Here the order of factor levels is important. For example, for the factor 'Treatment' given
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
170 in above table, edgeR computes fold changes of 'Treated' samples against 'Untreated',
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
171 i.e. the values correspond to up or down regulations of genes in Treated samples.
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
172
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
173 **Output**
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
174
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
175 edgeR_ generates a tabular file containing the different columns and results visualized in
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
176 a PDF:
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
177
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
178 ====== =============================================================================
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
179 Column Description
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
180 ------ -----------------------------------------------------------------------------
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
181 1 Tag (transposon element ID)
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
182 2 the logarithm (to basis 2) of the fold change (See the note in inputs section)
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
183 3 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
184 which controls false discovery rate (FDR)
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
185 4 Class the transposon belongs to
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
186 5 Type the transposon belongs to
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
187 ====== =============================================================================
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
188
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
189 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
190 ]]>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
191
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
192 **Note**: This edgeR_ wrapper was adapted from code available at
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
193 https://github.com/nskvir/RepEnrich
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
194
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
195 </help>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
196 <citations>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
197 <citation type="doi">10.1093/bioinformatics/btp616</citation>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
198 </citations>
6d59fbca2db4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
artbio
parents:
diff changeset
199 </tool>