Mercurial > repos > iuc > deseq2
annotate deseq2.xml @ 17:d9e5cadc7f0b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
author | iuc |
---|---|
date | Wed, 05 Sep 2018 15:54:03 -0400 |
parents | a416957ee305 |
children | 3bf1b3ec1ddf |
rev | line source |
---|---|
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
1 <tool id="deseq2" name="DESeq2" version="2.11.40.2"> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
2 <description>Determines differentially expressed features from count tables</description> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
3 <requirements> |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
4 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement> |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
5 <requirement type="package" version="1.6.0">bioconductor-tximport</requirement> |
13
3660c9088494
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c2e762b248fa86bb844c8e2d136e127d701d7b5a
iuc
parents:
12
diff
changeset
|
6 <requirement type="package" version="1.30.0">bioconductor-genomicfeatures</requirement> |
12
bd06df00180a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418
iuc
parents:
11
diff
changeset
|
7 <requirement type="package" version="0.6.5">r-ggrepel</requirement> |
bd06df00180a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418
iuc
parents:
11
diff
changeset
|
8 <requirement type="package" version="1.0.8">r-pheatmap</requirement> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
9 </requirements> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
10 <stdio> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
11 <regex match="Execution halted" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
12 source="both" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
13 level="fatal" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
14 description="Execution halted." /> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
15 <regex match="Error in" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
16 source="both" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
17 level="fatal" |
7
cb23006f34ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82d6e2f33ec7b26276715e01c5b17944a0f5cd0f
iuc
parents:
6
diff
changeset
|
18 description="An undefined error occurred, please check your input carefully and contact your administrator." /> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
19 <regex match="Fatal error" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
20 source="both" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
21 level="fatal" |
7
cb23006f34ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82d6e2f33ec7b26276715e01c5b17944a0f5cd0f
iuc
parents:
6
diff
changeset
|
22 description="An undefined error occurred, please check your input carefully and contact your administrator." /> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
23 </stdio> |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
24 <version_command><![CDATA[ |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
25 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
26 ]]></version_command> |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
27 <command><![CDATA[ |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
28 #if $tximport.tximport_selector == 'tximport': |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
29 #if $tximport.mapping_format.mapping_format_selector == 'gtf': |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
30 ln -s '$tximport.mapping_format.gtf_file' mapping.gtf && |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
31 #else: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
32 ln -s '$tximport.mapping_format.tabular_file' mapping.txt && |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
33 #end if |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
34 #end if |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
35 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
36 #import json |
12
bd06df00180a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418
iuc
parents:
11
diff
changeset
|
37 #import os |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
38 Rscript '${__tool_directory__}/deseq2.R' |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
39 -o '$deseq_out' |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
40 #if $pdf: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
41 -p '$plots' |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
42 #end if |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
43 #if $normCounts: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
44 -n '$counts_out' |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
45 #end if |
12
bd06df00180a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418
iuc
parents:
11
diff
changeset
|
46 #set $filename_to_element_identifiers = {} |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
47 #set $temp_factor_names = list() |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
48 #for $factor in $rep_factorName: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
49 #set $temp_factor = list() |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
50 #for $level in $factor.rep_factorLevel: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
51 #set $count_files = list() |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
52 #for $file in $level.countsFile: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
53 $count_files.append(str($file)) |
12
bd06df00180a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418
iuc
parents:
11
diff
changeset
|
54 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
55 #end for |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
56 $temp_factor.append( {str($level.factorLevel): $count_files} ) |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
57 #end for |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
58 $temp_factor.reverse() |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
59 $temp_factor_names.append([str($factor.factorName), $temp_factor]) |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
60 #end for |
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
61 |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
62 $header |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
63 |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
64 -f '#echo json.dumps(temp_factor_names)#' |
12
bd06df00180a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418
iuc
parents:
11
diff
changeset
|
65 -l '#echo json.dumps(filename_to_element_identifiers)#' |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
66 -t $fit_type |
17
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
67 #if $batch_factors |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
68 --batch_factors '$batch_factors' |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
69 #end if |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
70 #if $outlier_replace_off: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
71 -a |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
72 #end if |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
73 #if $outlier_filter_off: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
74 -b |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
75 #end if |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
76 #if $auto_mean_filter_off: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
77 -c |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
78 #end if |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
79 #if $many_contrasts: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
80 -m |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
81 #end if |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
82 #if $tximport.tximport_selector == 'tximport': |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
83 -i |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
84 -y $tximport.txtype |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
85 #if $tximport.mapping_format.mapping_format_selector == 'gtf': |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
86 -x mapping.gtf |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
87 #else: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
88 -x mapping.txt |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
89 #end if |
5
d38fd393402e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit da90fed6a52526d14b5e58fc3c5e7e8448d783d7
iuc
parents:
4
diff
changeset
|
90 |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
91 #end if |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
92 ]]></command> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
93 <inputs> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
94 <repeat name="rep_factorName" title="Factor" min="1"> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
95 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers" |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
96 help="Only letters, numbers and underscores will be retained in this field"> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
97 <sanitizer> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
98 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
99 </sanitizer> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
100 </param> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
101 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
102 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
103 help="Only letters, numbers and underscores will be retained in this field"> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
104 <sanitizer> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
105 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
106 </sanitizer> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
107 </param> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
108 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
109 </repeat> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
110 </repeat> |
17
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
111 <param name="batch_factors" type="data" format="tabular" optional="true" label="(Optional) provide a tabular file with additional batch factors to include in the model." help="You can produce this file using RUVSeq or svaseq."/> |
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
112 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" /> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
113 |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
114 <conditional name="tximport"> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
115 <param name="tximport_selector" type="select" label="Choice of Input data"> |
14
d0c39b5e78cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e811a7887db870f4f94f620f52bce656c8d5ba23
iuc
parents:
13
diff
changeset
|
116 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option> |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
117 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
118 </param> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
119 <when value="tximport"> |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
120 <param name="txtype" type="select" label="Program used to generate TPMs"> |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
121 <option value="kallisto">kallisto</option> |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
122 <option value="sailfish">Sailfish</option> |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
123 <option value="salmon">Salmon</option> |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
124 </param> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
125 <conditional name="mapping_format"> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
126 <param name="mapping_format_selector" type="select" label="Gene mapping format"> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
127 <option value="gtf" selected="True">GTF</option> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
128 <option value="tabular">Transcript-ID and Gene-ID mapping file</option> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
129 </param> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
130 <when value="gtf"> |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
131 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 file with Transcript - Gene mapping"/> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
132 </when> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
133 <when value="tabular"> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
134 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
135 </when> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
136 </conditional> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
137 </when> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
138 <when value="count" /> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
139 </conditional> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
140 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
141 label="Visualising the analysis results" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
142 help="output an additional PDF files" /> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
143 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
144 label="Output normalized counts table" /> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
145 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
146 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
147 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
148 <param name="fit_type" type="select" label="Fit type"> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
149 <option value="1" selected="true">parametric</option> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
150 <option value="2">local</option> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
151 <option value="3">mean</option> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
152 </param> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
153 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
154 label="Turn off outliers replacement (only affects with >6 replicates)" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
155 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
156 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
157 or normalization factor for that sample" /> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
158 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
159 label="Turn off outliers filtering (only affects with >2 replicates)" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
160 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
161 filter genes which contain a Cook’s distance above a cutoff" /> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
162 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
163 label="Turn off independent filtering" |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
164 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
165 </inputs> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
166 <outputs> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
167 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}"> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
168 <filter>many_contrasts is False</filter> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
169 <actions> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
170 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" /> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
171 </actions> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
172 </data> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
173 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}"> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
174 <filter>many_contrasts is True</filter> |
3
248e9c78346e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents:
2
diff
changeset
|
175 <discover_datasets pattern="None.(?P<designation>.+_vs_.+)" format="tabular" directory="." visible="false"/> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
176 </collection> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
177 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}"> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
178 <filter>pdf == True</filter> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
179 </data> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
180 <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}"> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
181 <filter>normCounts == True</filter> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
182 </data> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
183 </outputs> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
184 <tests> |
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
185 <!--Ensure counts files with header works --> |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
186 <test expect_num_outputs="2"> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
187 <repeat name="rep_factorName"> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
188 <param name="factorName" value="Treatment"/> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
189 <repeat name="rep_factorLevel"> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
190 <param name="factorLevel" value="Treated"/> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
191 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
192 </repeat> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
193 <repeat name="rep_factorLevel"> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
194 <param name="factorLevel" value="Untreated"/> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
195 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
196 </repeat> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
197 </repeat> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
198 <param name="pdf" value="False"/> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
199 <param name="normCounts" value="True"/> |
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
200 <output name="counts_out"> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
201 <assert_contents> |
16
a416957ee305
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 81fa5b04b9ba9d4b1b59192af0adb1e1e18ca22b
iuc
parents:
15
diff
changeset
|
202 <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts" /> |
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
203 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" /> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
204 </assert_contents> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
205 </output> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
206 <output name="deseq_out" > |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
207 <assert_contents> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
208 <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" /> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
209 </assert_contents> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
210 </output> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
211 </test> |
17
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
212 <!--Ensure additional batch factor correction works --> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
213 <test expect_num_outputs="2"> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
214 <repeat name="rep_factorName"> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
215 <param name="factorName" value="Treatment"/> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
216 <repeat name="rep_factorLevel"> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
217 <param name="factorLevel" value="Treated"/> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
218 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
219 </repeat> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
220 <repeat name="rep_factorLevel"> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
221 <param name="factorLevel" value="Untreated"/> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
222 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
223 </repeat> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
224 </repeat> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
225 <param name="batch_factors" value="batch_factors.tab"/> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
226 <param name="pdf" value="False"/> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
227 <param name="normCounts" value="True"/> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
228 <output name="deseq_out"> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
229 <assert_contents> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
230 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149" /> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
231 </assert_contents> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
232 </output> |
d9e5cadc7f0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
16
diff
changeset
|
233 </test> |
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
234 <!--Ensure counts files without header works --> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
235 <test expect_num_outputs="2"> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
236 <repeat name="rep_factorName"> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
237 <param name="factorName" value="Treatment"/> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
238 <repeat name="rep_factorLevel"> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
239 <param name="factorLevel" value="Treated"/> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
240 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
241 </repeat> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
242 <repeat name="rep_factorLevel"> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
243 <param name="factorLevel" value="Untreated"/> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
244 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
245 </repeat> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
246 </repeat> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
247 <param name="header" value="False"/> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
248 <param name="pdf" value="False"/> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
249 <param name="normCounts" value="True"/> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
250 <output name="counts_out"> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
251 <assert_contents> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
252 <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader" /> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
253 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" /> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
254 </assert_contents> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
255 </output> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
256 <output name="deseq_out" > |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
257 <assert_contents> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
258 <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" /> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
259 </assert_contents> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
260 </output> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
261 </test> |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
262 <!--Ensure Sailfish/Salmon input with tx2gene table works--> |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
263 <test expect_num_outputs="1"> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
264 <repeat name="rep_factorName"> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
265 <param name="factorName" value="Treatment"/> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
266 <repeat name="rep_factorLevel"> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
267 <param name="factorLevel" value="Treated"/> |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
268 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
269 </repeat> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
270 <repeat name="rep_factorLevel"> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
271 <param name="factorLevel" value="Untreated"/> |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
272 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/> |
6
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
273 </repeat> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
274 </repeat> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
275 <param name="pdf" value="False"/> |
4939397c4706
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
5
diff
changeset
|
276 <param name="tximport_selector" value="tximport"/> |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
277 <param name="txtype" value="sailfish"/> |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
278 <param name="mapping_format_selector" value="tabular"/> |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
279 <param name="tabular_file" value="tx2gene.tab"/> |
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
280 <output name="deseq_out" > |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
281 <assert_contents> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
282 <has_text_matching expression="MIR6859-2\t1.1858.*\t-1.5832.*\t1.2956.*\t-1.2219.*\t0.2217.*\t0.8868.*" /> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
283 </assert_contents> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
284 </output> |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
285 </test> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
286 </tests> |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
287 <help><![CDATA[ |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
288 .. class:: infomark |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
289 |
3
248e9c78346e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents:
2
diff
changeset
|
290 **What it does** |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
291 |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
292 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
293 |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
294 ----- |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
295 |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
296 **Inputs** |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
297 |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
298 **Count Files** |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
299 |
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
300 DESeq2_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually. One header row is assumed, but files with no header (e.g from HTSeq) can be input with the *Files have header?* option set to No. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might 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. You need to select appropriate count table from your history for each factor level. |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
301 |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
302 The following table gives some examples of factors and their levels: |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
303 |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
304 ========= ============== =============== |
3
248e9c78346e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents:
2
diff
changeset
|
305 Factor Factor level 1 Factor level 2 |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
306 --------- -------------- --------------- |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
307 Treatment Treated Untreated |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
308 --------- -------------- --------------- |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
309 Condition Knockdown Wildtype |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
310 --------- -------------- --------------- |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
311 TimePoint Day4 Day1 |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
312 --------- -------------- --------------- |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
313 SeqType SingleEnd PairedEnd |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
314 --------- -------------- --------------- |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
315 Gender Female Male |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
316 ========= ============== =============== |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
317 |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
318 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'Treatment' given in above table, DESeq2 computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples. |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
319 |
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
320 DESeq2_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2. |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
321 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
322 **Salmon or Sailfish Files** |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
323 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
324 Salmon or Sailfish ``quant.sf`` files can be imported by setting type to *Salmon* or *Sailfish* respectively above. Note: for previous version of Salmon or Sailfish, in which the quant.sf files start with comment lines you will need to remove the comment lines before inputting here. An example of the format is shown below. |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
325 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
326 Example: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
327 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
328 ============ ========== =============== =========== =========== |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
329 Name Length EffectiveLength TPM NumReads |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
330 ------------ ---------- --------------- ----------- ----------- |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
331 NR_001526 164 20.4518 0 0 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
332 NR_001526_1 164 20.4518 0 0 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
333 NR_001526_2 164 20.4518 0 0 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
334 NM_130786 1764 1956.04 2.47415 109.165 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
335 NR_015380 2129 2139.53 1.77331 85.5821 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
336 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
337 NM_001198819 9527 7964.62 0 0 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
338 NM_001198820 9410 7855.78 0 0 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
339 NM_014576 9267 7714.88 0.0481114 8.37255 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
340 ============ ========== =============== =========== =========== |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
341 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
342 **kallisto Files** |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
343 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
344 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below. |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
345 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
346 Example: |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
347 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
348 ============ ========== =============== =========== =========== |
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
349 target_id length eff_length est_counts tpm |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
350 ------------ ---------- --------------- ----------- ----------- |
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
351 NR_001526 164 20.4518 0 0 |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
352 NR_001526_1 164 20.4518 0 0 |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
353 NR_001526_2 164 20.4518 0 0 |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
354 NM_130786 1764 1956.04 109.165 2.47415 |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
355 NR_015380 2129 2139.53 85.5821 1.77331 |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
356 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07 |
15
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
357 NM_001198819 9527 7964.62 0 0 |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
358 NM_001198820 9410 7855.78 0 0 |
9a616afdbda5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents:
14
diff
changeset
|
359 NM_014576 9267 7714.88 8.37255 0.0481114 |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
360 ============ ========== =============== =========== =========== |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
361 |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
362 ----- |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
363 |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
364 **Output** |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
365 |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
366 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF. |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
367 |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
368 ====== ========================================================== |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
369 Column Description |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
370 ------ ---------------------------------------------------------- |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
371 1 Gene Identifiers |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
372 2 mean normalised counts, averaged over all samples from both conditions |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
373 3 the logarithm (to basis 2) of the fold change (See the note in inputs section) |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
374 4 standard error estimate for the log2 fold change estimate |
2
afe2a77c5900
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e0f819a2fd56eb5ee30a7fd772780693e1f085fa
iuc
parents:
1
diff
changeset
|
375 5 Wald statistic |
afe2a77c5900
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e0f819a2fd56eb5ee30a7fd772780693e1f085fa
iuc
parents:
1
diff
changeset
|
376 6 p value for the statistical significance of this change |
afe2a77c5900
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e0f819a2fd56eb5ee30a7fd772780693e1f085fa
iuc
parents:
1
diff
changeset
|
377 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
378 which controls false discovery rate (FDR) |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
379 ====== ========================================================== |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
380 |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
381 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html |
11
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
382 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html |
25204a860b79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents:
10
diff
changeset
|
383 ]]></help> |
0
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
384 <citations> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
385 <citation type="doi">10.1186/s13059-014-0550-8</citation> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
386 </citations> |
d983d19fbbab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff
changeset
|
387 </tool> |