Mercurial > repos > drosofff > repenrich

annotate edger-repenrich.xml @ 1:54a3f3a195d6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
author drosofff
date Mon, 29 May 2017 13:11:57 -0400
parents
children aed130b47d36
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
1 <tool id="edger-repenrich" name="edgeR-repenrich" version="0.3.0">
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
2 <description>Determines differentially expressed features from RepEnrich counts</description>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
3 <requirements>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
4 <requirement type="package" version="3.16.5-r3.3.1_0">bioconductor-edger</requirement>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
5 <requirement type="package" version="3.30.13-r3.3.1_0">bioconductor-limma</requirement>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
6 <requirement type="package" version="1.20.0-r3.3.1_0">r-getopt</requirement>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
7 <requirement type="package" version="0.2.15-r3.3.1_0">r-rjson</requirement>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
8 </requirements>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
9 <stdio>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
10 <regex match="Execution halted"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
11 source="both"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
12 level="fatal"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
13 description="Execution halted." />
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
14 <regex match="Error in"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
15 source="both"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
16 level="fatal"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
17 description="An undefined error occurred, please check your input carefully and contact your administrator." />
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
18 <regex match="Fatal error"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
19 source="both"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
20 level="fatal"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
21 description="An undefined error occurred, please check your input carefully and contact your administrator." />
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
22 </stdio>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
23 <version_command>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
24 <![CDATA[
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
25 echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR) &&
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
26 cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
27 ]]>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
28 </version_command>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
29 <command>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
30 <![CDATA[
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
31 #import json
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
32 Rscript '${__tool_directory__}/edgeR_repenrich.R'
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
33 --factorName '$factorName'
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
34
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
35 --levelNameA '$factorLevel_A'
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
36 #set $factorlevelsA = list()
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
37 #for $file in $countsFiles_A:
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
38 $factorlevelsA.append(str($file))
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
39 #end for
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
40 $factorlevelsA.reverse()
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
41 --levelAfiles '#echo json.dumps(factorlevelsA)#'
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
42
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
43 --levelNameB '$factorLevel_B'
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
44 #set $factorlevelsB = list()
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
45 #for $file in $countsFiles_B:
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
46 $factorlevelsB.append(str($file))
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
47 #end for
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
48 $factorlevelsB.reverse()
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
49 --levelBfiles '#echo json.dumps(factorlevelsB)#'
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
50
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
51 #set $alignedA = list()
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
52 #for file in $alignmentFiles_A:
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
53 $alignedA.append(str($file))
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
54 #end for
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
55 $alignedA.reverse()
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
56 --alignmentA '#echo json.dumps(alignedA)#'
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
57
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
58 #set $alignedB = list()
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
59 #for file in $alignmentFiles_B:
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
60 $alignedB.append(str($file))
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
61 #end for
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
62 $alignedB.reverse()
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
63 --alignmentB '#echo json.dumps(alignedB)#'
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
64
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
65 -o 'edger_out'
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
66
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
67 -p '$plots'
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
68 #if $normCounts:
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
69 -n '$counts_out'
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
70 #end if
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
71 -o '$edger_out'
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
72 ]]>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
73 </command>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
74 <inputs>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
75 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. genotype or age or drug_x"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
76 help="Only letters, numbers and underscores will be retained in this field">
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
77 <sanitizer>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
78 <valid initial="string.letters,string.digits"><add value="_" /></valid>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
79 </sanitizer>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
80 </param>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
81 <param name="factorLevel_A" type="text" value="FactorLevel1" label="Specify a factor level, typical values could be 'wildtype' or 'control'"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
82 help="Only letters, numbers and underscores will be retained in this field">
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
83 <sanitizer>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
84 <valid initial="string.letters,string.digits"><add value="_" /></valid>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
85 </sanitizer>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
86 </param>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
87 <param name="countsFiles_A" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich" />
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
88 <param name="alignmentFiles_A" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
89 <param name="factorLevel_B" type="text" value="FactorLevel2" label="Specify a factor level, typical values could be 'mutant' or 'Drug_X'"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
90 help="Only letters, numbers and underscores will be retained in this field">
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
91 <sanitizer>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
92 <valid initial="string.letters,string.digits"><add value="_" /></valid>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
93 </sanitizer>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
94 </param>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
95 <param name="countsFiles_B" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich tool" />
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
96 <param name="alignmentFiles_B" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
97 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
98 label="Output normalized counts table" />
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
99 </inputs>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
100 <outputs>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
101 <data format="tabular" name="edger_out" label="edgeR result file on ${on_string}">
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
102 <actions>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
103 <action name="column_names" type="metadata" default="Tag,log2(FC),FDR,Class,Type" />
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
104 </actions>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
105 </data>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
106 <data format="pdf" name="plots" label="edgeR plots on ${on_string}" />
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
107 <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}">
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
108 <filter>normCounts == True</filter>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
109 </data>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
110 </outputs>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
111 <tests>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
112 <test>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
113 <param name="factorName" value="genotype"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
114 <param name="factorLevel_A" value="wildtype"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
115 <param name="countsFiles_A" value="353_fraction_counts.tab,354_fraction_counts.tab"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
116 <param name="alignmentFiles_A" value="aligned_353.tab,aligned_354.tab"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
117 <param name="factorLevel_B" value="mutant"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
118 <param name="countsFiles_B" value="355_fraction_counts.tab,356_fraction_counts.tab"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
119 <param name="alignmentFiles_B" value="aligned_355.tab,aligned_356.tab"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
120 <param name="normCounts" value="True"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
121 <output name="counts_out" file="Normalized_counts_file.tab"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
122 <output name="plots" file="edgeR_plots.pdf"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
123 <output name="edger_out" file="edgeR_result_file.tab"/>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
124
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
125 </test>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
126 </tests>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
127 <help>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
128 <![CDATA[
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
129 .. class:: infomark
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
130
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
131 **What it does**
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
132
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
133 Estimate Distance between samples (MDS) and Biological Coefficient Variation (BCV) in count data from high-throughput sequencing assays and test for differential expression using edgeR_.
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
134
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
135 **Inputs**
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
136
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
137 edger-repenrich takes count tables generated by repenrich as input. Count tables must be generated for each sample individually. Here, edgeR_ is handling a single factor (genotype, age, treatment, etc) that effect your experiment. This factor has two levels/states (for instance, "wild-type" and "mutant".
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
138 You need to select appropriate count table from your history for each factor level.
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
139
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
140 The following table gives some examples of factors and their levels:
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
141
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
142 ========= ============== ===============
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
143 Factor Factorlevel1 Factorlevel2
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
144 --------- -------------- ---------------
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
145 Treatment Treated Untreated
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
146 --------- -------------- ---------------
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
147 Genotype Knockdown Wildtype
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
148 --------- -------------- ---------------
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
149 TimePoint Day4 Day1
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
150 --------- -------------- ---------------
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
151 Gender Female Male
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
152 ========= ============== ===============
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
153
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
154 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'Treatment' given in above table, DESeq2 computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples.
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
155
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
156 **Output**
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
157
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
158 edgeR_ generates a tabular file containing the different columns and results visualized in a PDF:
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
159
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
160 ====== =============================================================================
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
161 Column Description
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
162 ------ -----------------------------------------------------------------------------
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
163 1 Tag (transposon element ID)
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
164 2 the logarithm (to basis 2) of the fold change (See the note in inputs section)
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
165 3 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
166 which controls false discovery rate (FDR)
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
167 4 Class the transposon belongs to
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
168 5 Type the transposon belongs to
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
169 ====== =============================================================================
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
170
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
171 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
172 ]]>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
173
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
174 **Note**: This edgeR_ wrapper was adapted from code available at https://github.com/nskvir/RepEnrich
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
175
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
176 </help>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
177 <citations>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
178 <citation type="doi">10.1093/bioinformatics/btp616</citation>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
179 </citations>
54a3f3a195d6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
drosofff
parents:
diff changeset
180 </tool>