Mercurial > repos > iuc > dexseq

annotate dexseq.xml @ 3:f89c9b25feb4 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 e785d126b23609208b055fb8902f3b9368e9b839
author iuc
date Sat, 28 Jul 2018 03:44:02 -0400
parents 6e8b61c54ff3
children 251393b72616
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
1 <tool id="dexseq" name="DEXSeq" version="@VERSION@.0">
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
2 <description>Determines differential exon usage from count tables</description>
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
3 <macros>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
4 <import>macros.xml</import>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
5 </macros>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
6 <expand macro="requirements">
1
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
7 <requirement type="package" version="1.20.0">r-getopt</requirement>
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
8 <requirement type="package" version="0.2.15">r-rjson</requirement>
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
9 </expand>
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
10 <code file="dexseq_helper.py" />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
11 <stdio>
1
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
12 <regex match="Execution halted"
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
13 source="both"
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
14 level="fatal"
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
15 description="Execution halted." />
1
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
16 <regex match="Input-Error 01"
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
17 source="both"
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
18 level="fatal"
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
19 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
20 <regex match="Error in"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
21 source="both"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
22 level="fatal"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
23 description="An undefined error occured, please check your input carefully and contact your administrator." />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
24 <regex match="Error:"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
25 source="both"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
26 level="fatal"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
27 description="Error in the R script." />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
28 </stdio>
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
29 <version_command><![CDATA[
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
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: ")")"
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
31 ]]></version_command>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
32 <command><![CDATA[
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
33 mkdir ./html_out &&
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
34 #import json
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
35 Rscript '$__tool_directory__/dexseq.R'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
36 -o '$dexseq_out'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
37 -p \${GALAXY_SLOTS:-4}
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
38 #set $temp_factor_names = list()
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
39 #for $factor in $rep_factorName:
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
40 #set $temp_factor = list()
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
41 #set $count_files1 = list()
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
42 #for $file in $factor.countFiles1:
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
43 $count_files1.append(str($file))
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
44 #end for
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
45 $temp_factor.append( {str($factor.factorLevel1): $count_files1} )
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
46
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
47 #set $count_files2 = list()
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
48 #for $file in $factor.countFiles2:
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
49 $count_files2.append(str($file))
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
50 #end for
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
51 $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
52 $temp_factor_names.append([str($factor.factorName), $temp_factor])
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
53 #end for
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
54 -f '#echo json.dumps(temp_factor_names)#'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
55 -a $gtf
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
56 -c $fdr_cutoff
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
57
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
58 #if $report:
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
59 -r ./html_out
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
60 &&
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
61 mkdir '$htmlreport.extra_files_path'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
62 &&
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
63 cp ./html_out/testForDEU.html $htmlreport
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
64 &&
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
65 cp -r ./html_out/* '$htmlreport.extra_files_path'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
66 #end if
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
67 ]]></command>
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
68 <inputs>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
69 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
70 <repeat name="rep_factorName" title="Factor" min="1">
1
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
71 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
72 help="Only letters, numbers and underscores will be retained in this field">
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
73 <sanitizer>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
74 <valid initial="string.letters,string.digits"><add value="_" /></valid>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
75 </sanitizer>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
76 </param>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
77 <param name="factorLevel1" type="text" value="FactorLevel1" label="Specify a factor level"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
78 help="Only letters, numbers and underscores will be retained in this field">
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
79 <sanitizer>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
80 <valid initial="string.letters,string.digits"><add value="_" /></valid>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
81 </sanitizer>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
82 </param>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
83 <param name="countFiles1" type="data" format="tabular" multiple="true" label="Count file for factor level 1"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
84
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
85 <param name="factorLevel2" type="text" value="FactorLevel2" label="Specify a factor level"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
86 help="Only letters, numbers and underscores will be retained in this field">
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
87 <sanitizer>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
88 <valid initial="string.letters,string.digits"><add value="_" /></valid>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
89 </sanitizer>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
90 </param>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
91 <param name="countFiles2" type="data" format="tabular" multiple="true" label="Count files for factor level 2"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
92 </repeat>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
93 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
94 label="Visualise the analysis results?"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
95 help="Output an additional HTML file." />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
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"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
97 </inputs>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
98 <outputs>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
99 <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}" />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
100 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
101 <filter>report is True</filter>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
102 </data>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
103 </outputs>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
104 <tests>
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
105 <!-- Ensure default output works-->
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
106 <test expect_num_outputs="1">
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
107 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
108 <repeat name="rep_factorName">
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
109 <param name="factorName" value="condition"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
110 <param name="factorLevel1" value="knockdown"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
111 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
112 <param name="factorLevel2" value="control"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
113 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
114 </repeat>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
115 <param name="report" value="False"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
116 <param name="fdr_cutoff" value="1"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
117 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
118 </test>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
119 <!-- Ensure report works-->
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
120 <test expect_num_outputs="2">
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
121 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
122 <repeat name="rep_factorName">
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
123 <param name="factorName" value="Treatment"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
124 <param name="factorLevel1" value="knockdown"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
125 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
126 <param name="factorLevel2" value="control"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
127 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
128 </repeat>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
129 <param name="report" value="True"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
130 <param name="fdr_cutoff" value="1"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
131 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
132 </test>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
133 <!-- Ensure two factors works-->
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
134 <test expect_num_outputs="1">
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
135 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
136 <repeat name="rep_factorName">
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
137 <param name="factorName" value="condition"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
138 <param name="factorLevel1" value="knockdown"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
139 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
140 <param name="factorLevel2" value="control"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
141 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
142 </repeat>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
143 <repeat name="rep_factorName">
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
144 <param name="factorName" value="libtype"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
145 <param name="factorLevel1" value="singleend"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
146 <param name="countFiles1" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt" ftype="tabular"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
147 <param name="factorLevel2" value="pairedend"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
148 <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
149 </repeat>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
150 <param name="report" value="False"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
151 <param name="fdr_cutoff" value="0.05"/>
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
152 <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular"/>
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
153 </test>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
154 </tests>
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
155 <help><![CDATA[
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
156 .. class:: infomark
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
157
1
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
158 **What it does**
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
159
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
160 Inference of differential exon usage in RNA-Seq.
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
161
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
162
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
163 **Inputs**
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
164
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
165 DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
167 factor that affects gene expressions. You also input several secondary factors that might
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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.
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
169 You need to select appropriate count table from your history for each factor level.
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
170
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
171 The following table gives some examples of factors and their levels:
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
172
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
173 ========= ============== ===============
1
f1c406f9554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
iuc
parents: 0
diff changeset
174 Factor Factor level 1 Factor level 2
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
175 --------- -------------- ---------------
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
176 condition Knockdown Wildtype
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
177 --------- -------------- ---------------
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
178 treatment Treated Untreated
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
179 --------- -------------- ---------------
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
180 timePoint Day4 Day1
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
181 --------- -------------- ---------------
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
182 SeqType SingleEnd PairedEnd
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
183 --------- -------------- ---------------
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
184 Gender Female Male
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
185 ========= ============== ===============
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
186
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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.
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
188
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
189 **Output**
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
190
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
191 DEXSeq_ generates a tabular file containing the different columns and an optional html report.
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
192
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
193 ====== ==========================================================
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
194 Column Description
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
195 ------ ----------------------------------------------------------
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
196 1 Gene and exon Identifiers
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
197 2 group/gene identifier
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
198 3 feature/exon identifier
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
199 4 mean of the counts across samples in each feature/exon
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
200 5 exon dispersion estimate
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
201 6 LRT statistic
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
202 7 LRT p-value
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
203 8 BH adjusted p-values
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
204 9 exon usage coefficient factorLevel 2
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
205 10 exon usage coefficient factorLevel 1
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
206 11 relative exon usage fold changes
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
207 12 GRanges object of the coordinates of the exon/feature
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
208 13 matrix of integer counts, of each column containing a sample
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
209 14 list of transcripts overlapping with the exon
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
210 ====== ==========================================================
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
211
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
212
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
213 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
2
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 1
diff changeset
214 ]]></help>
0
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
215 <citations>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
216 <citation type="doi">10.1101/gr.133744.111</citation>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
217 </citations>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
diff changeset
218 </tool>