Mercurial > repos > iuc > dexseq

annotate dexseq.xml @ 8:0ccbed58b270 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
author iuc
date Sun, 28 Jan 2018 04:03:29 -0500
parents 469c0d7489bd
children 6f684b3b0a6d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
1 <tool id="dexseq" name="DEXSeq" version="@VERSION@.0">
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
2 <description>Determines differential exon usage from count tables</description>
8
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
3 <macros>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
4 <import>macros.xml</import>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
5 </macros>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
6 <expand macro="requirements">
7
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 5
diff changeset
7 <requirement type="package" version="1.20.0">r-getopt</requirement>
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 5
diff changeset
8 <requirement type="package" version="0.2.15">r-rjson</requirement>
8
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
9 </expand>
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
10 <code file="dexseq_helper.py" />
3
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
iuc
parents: 2
diff changeset
11 <stdio>
7
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 5
diff changeset
12 <regex match="Execution halted"
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 5
diff changeset
13 source="both"
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 5
diff changeset
14 level="fatal"
3
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
iuc
parents: 2
diff changeset
15 description="Execution halted." />
7
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 5
diff changeset
16 <regex match="Input-Error 01"
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 5
diff changeset
17 source="both"
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 5
diff changeset
18 level="fatal"
3
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
iuc
parents: 2
diff changeset
19 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
4
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
iuc
parents: 3
diff changeset
20 <regex match="Error in"
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
iuc
parents: 3
diff changeset
21 source="both"
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
iuc
parents: 3
diff changeset
22 level="fatal"
5
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
23 description="An undefined error occured, please check your input carefully and contact your administrator." />
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
24 <regex match="Error:"
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
25 source="both"
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
26 level="fatal"
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
27 description="Error in the R script." />
3
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
iuc
parents: 2
diff changeset
28 </stdio>
8
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
29 <version_command><![CDATA[
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
30 echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
31 ]]></version_command>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
32 <command><![CDATA[
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
33 mkdir ./html_out &&
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
34 #import json
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
35 Rscript '$__tool_directory__/dexseq.R'
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
36 -o '$dexseq_out'
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
37 -p \${GALAXY_SLOTS:-4}
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
38 #set $temp_factor_names = list()
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
39 #for $factor in $rep_factorName:
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
40 #set $temp_factor = list()
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
41 #set $count_files1 = list()
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
42 #for $file in $factor.countFiles1:
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
43 $count_files1.append(str($file))
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
44 #end for
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
45 $temp_factor.append( {str($factor.factorLevel1): $count_files1} )
5
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
46
8
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
47 #set $count_files2 = list()
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
48 #for $file in $factor.countFiles2:
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
49 $count_files2.append(str($file))
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
50 #end for
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
51 $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
52 $temp_factor_names.append([str($factor.factorName), $temp_factor])
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
53 #end for
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
54 -f '#echo json.dumps(temp_factor_names)#'
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
55 -a $gtf
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
56 -c $fdr_cutoff
4
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
iuc
parents: 3
diff changeset
57
8
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
58 #if $report:
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
59 -r ./html_out
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
60 &&
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
61 mkdir '$htmlreport.extra_files_path'
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
62 &&
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
63 cp ./html_out/testForDEU.html $htmlreport
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
64 &&
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
65 cp -r ./html_out/* '$htmlreport.extra_files_path'
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
66 #end if
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
67 ]]></command>
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
68 <inputs>
3
a26a82bed63f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
iuc
parents: 2
diff changeset
69 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
70 <repeat name="rep_factorName" title="Factor" min="1">
7
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 5
diff changeset
71 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
72 help="Only letters, numbers and underscores will be retained in this field">
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
73 <sanitizer>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
74 <valid initial="string.letters,string.digits"><add value="_" /></valid>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
75 </sanitizer>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
76 </param>
5
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
77 <param name="factorLevel1" type="text" value="FactorLevel1" label="Specify a factor level"
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
78 help="Only letters, numbers and underscores will be retained in this field">
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
79 <sanitizer>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
80 <valid initial="string.letters,string.digits"><add value="_" /></valid>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
81 </sanitizer>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
82 </param>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
83 <param name="countFiles1" type="data" format="tabular" multiple="true" label="Count file for factor level 1"/>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
84
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
85 <param name="factorLevel2" type="text" value="FactorLevel2" label="Specify a factor level"
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
86 help="Only letters, numbers and underscores will be retained in this field">
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
87 <sanitizer>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
88 <valid initial="string.letters,string.digits"><add value="_" /></valid>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
89 </sanitizer>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
90 </param>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
91 <param name="countFiles2" type="data" format="tabular" multiple="true" label="Count files for factor level 2"/>
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
92 </repeat>
4
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
iuc
parents: 3
diff changeset
93 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
94 label="Visualise the analysis results?"
4
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
iuc
parents: 3
diff changeset
95 help="Output an additional HTML file." />
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
iuc
parents: 3
diff changeset
96 <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
97 </inputs>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
98 <outputs>
4
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
iuc
parents: 3
diff changeset
99 <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}" />
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
100 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
4
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
iuc
parents: 3
diff changeset
101 <filter>report is True</filter>
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
102 </data>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
103 </outputs>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
104 <tests>
8
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
105 <!-- Ensure default output works-->
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
106 <test expect_num_outputs="1">
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
107 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
108 <repeat name="rep_factorName">
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
109 <param name="factorName" value="condition"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
110 <param name="factorLevel1" value="knockdown"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
111 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
112 <param name="factorLevel2" value="control"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
113 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
114 </repeat>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
115 <param name="report" value="False"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
116 <param name="fdr_cutoff" value="1"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
117 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
118 </test>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
119 <!-- Ensure report works-->
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
120 <test expect_num_outputs="2">
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
121 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
122 <repeat name="rep_factorName">
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
123 <param name="factorName" value="Treatment"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
124 <param name="factorLevel1" value="knockdown"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
125 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
126 <param name="factorLevel2" value="control"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
127 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
128 </repeat>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
129 <param name="report" value="True"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
130 <param name="fdr_cutoff" value="1"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
131 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
132 </test>
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
133 <!-- Ensure two factors works-->
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
134 <test expect_num_outputs="1">
5
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
135 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
136 <repeat name="rep_factorName">
4
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
iuc
parents: 3
diff changeset
137 <param name="factorName" value="condition"/>
5
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
138 <param name="factorLevel1" value="knockdown"/>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
139 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
140 <param name="factorLevel2" value="control"/>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
141 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
142 </repeat>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
143 <repeat name="rep_factorName">
4
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
iuc
parents: 3
diff changeset
144 <param name="factorName" value="libtype"/>
5
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
145 <param name="factorLevel1" value="singleend"/>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
146 <param name="countFiles1" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt" ftype="tabular"/>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
147 <param name="factorLevel2" value="pairedend"/>
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
148 <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
149 </repeat>
4
7069d55968fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267
iuc
parents: 3
diff changeset
150 <param name="report" value="False"/>
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
151 <param name="fdr_cutoff" value="0.05"/>
8
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
152 <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular"/>
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
153 </test>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
154 </tests>
8
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
155 <help><![CDATA[
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
156 .. class:: infomark
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
157
7
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 5
diff changeset
158 **What it does**
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
159
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
160 Inference of differential exon usage in RNA-Seq.
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
161
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
162
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
163 **Inputs**
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
164
5
28a2181df3b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents: 4
diff changeset
165 DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
166 DEXSeq_ is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary
8
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
167 factor that affects gene expressions. You also input several secondary factors that might
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
168 influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states.
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
169 You need to select appropriate count table from your history for each factor level.
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
170
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
171 The following table gives some examples of factors and their levels:
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
172
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
173 ========= ============== ===============
7
469c0d7489bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 5
diff changeset
174 Factor Factor level 1 Factor level 2
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
175 --------- -------------- ---------------
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
176 condition Knockdown Wildtype
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
177 --------- -------------- ---------------
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
178 treatment Treated Untreated
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
179 --------- -------------- ---------------
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
180 timePoint Day4 Day1
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
181 --------- -------------- ---------------
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
182 SeqType SingleEnd PairedEnd
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
183 --------- -------------- ---------------
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
184 Gender Female Male
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
185 ========= ============== ===============
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
186
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
187 *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 'condition' given in above table, DEXSeq computes fold changes of 'Knockdown' samples against 'Wildtype', i.e. the values correspond to up or down regulations of genes in Knockdown samples.
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
188
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
189 **Output**
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
190
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
191 DEXSeq_ generates a tabular file containing the different columns and an optional html report.
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
192
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
193 ====== ==========================================================
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
194 Column Description
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
195 ------ ----------------------------------------------------------
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
196 1 Gene and exon Identifiers
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
197 2 group/gene identifier
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
198 3 feature/exon identifier
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
199 4 mean of the counts across samples in each feature/exon
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
200 5 exon dispersion estimate
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
201 6 LRT statistic
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
202 7 LRT p-value
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
203 8 BH adjusted p-values
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
204 9 exon usage coefficient factorLevel 2
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
205 10 exon usage coefficient factorLevel 1
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
206 11 relative exon usage fold changes
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
207 12 GRanges object of the coordinates of the exon/feature
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
208 13 matrix of integer counts, of each column containing a sample
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
209 14 list of transcripts overlapping with the exon
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
210 ====== ==========================================================
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
211
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
212
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
213 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
8
0ccbed58b270 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 7
diff changeset
214 ]]></help>
0
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
215 <citations>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
216 <citation type="doi">10.1101/gr.133744.111</citation>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
217 </citations>
276833129f97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit eecb633ff51d61e8f94f580bb96053434029ab78-dirty
iuc
parents:
diff changeset
218 </tool>