Mercurial > repos > iuc > deseq2

annotate deseq2.xml @ 26:6a3a025714d3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0b502ee6bfa3e861c8678cabfeb670dc8dfe9519"
author iuc
date Fri, 08 Jan 2021 20:29:54 +0000
parents de44f8eff84a
children d027d1f4984e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
24
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
1 <tool id="deseq2" name="DESeq2" version="2.11.40.6+galaxy1">
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>
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
3 <macros>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
4 <import>deseq2_macros.xml</import>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
5 </macros>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
6 <requirements>
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
7 <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
8 <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
9 <requirement type="package" version="2.26.2">bioconductor-rhdf5</requirement>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
10 <requirement type="package" version="1.10.0">bioconductor-tximport</requirement>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
11 <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
12 <requirement type="package" version="1.20.2">r-getopt</requirement>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
13 <requirement type="package" version="0.8.0">r-ggrepel</requirement>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
14 <requirement type="package" version="3.0.1">r-gplots</requirement>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
15 <requirement type="package" version="1.0.10">r-pheatmap</requirement>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
16 <requirement type="package" version="0.2.20">r-rjson</requirement>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
17 </requirements>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
18 <stdio>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
19 <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
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"
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
22 description="Execution halted." />
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
23 <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
24 source="both"
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
25 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
26 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
27 <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
28 source="both"
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
29 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
30 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
31 </stdio>
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
32 <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
33 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
34 ]]></version_command>
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
35 <command><![CDATA[
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
36 #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
37 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
38 ln -s '$tximport.mapping_format.gtf_file' mapping.gff &&
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
39 #else:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
40 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
41 #end if
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
42 #end if
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
43
26
6a3a025714d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0b502ee6bfa3e861c8678cabfeb670dc8dfe9519"
iuc
parents: 25
diff changeset
44 ## This is needed for Pulsar to transfer the file
6a3a025714d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0b502ee6bfa3e861c8678cabfeb670dc8dfe9519"
iuc
parents: 25
diff changeset
45 cat '$__tool_directory__/get_deseq_dataset.R' > /dev/null &&
6a3a025714d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0b502ee6bfa3e861c8678cabfeb670dc8dfe9519"
iuc
parents: 25
diff changeset
46
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
47 #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
48 #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
49 Rscript '${__tool_directory__}/deseq2.R'
21
a6fc9228e1a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 05bc13637dc9f8e523bc72844ff6eb0794f98ad3
iuc
parents: 20
diff changeset
50 --cores \${GALAXY_SLOTS:-1}
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
51 -o '$deseq_out'
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
52 #if $pdf:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
53 -p '$plots'
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
54 #end if
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
55 #if $normCounts:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
56 -n '$counts_out'
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
57 #end if
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
58 #if $normRLog:
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
59 -r '$rlog_out'
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
60 #end if
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
61 #if $normVST:
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
62 -v '$vst_out'
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
63 #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
64 #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
65 #set $temp_factor_names = list()
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
66 #for $factor in $select_data.rep_factorName:
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
67 #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
68 #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
69 #set $count_files = list()
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
70 #if $select_data.how == 'group_tags':
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
71 #for $group in $level.groups.value:
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
72 #for $file in $select_data.countsFile.get_datasets_for_group($group):
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
73 $count_files.append(str($file))
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
74 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
75 #end for
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
76 #end for
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
77 #else:
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
78 #for $file in $level.countsFile:
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
79 $count_files.append(str($file))
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
80 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
81 #end for
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
82 #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
83 $temp_factor.append( {str($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
84 #end for
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
85 $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
86 $temp_factor_names.append([str($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
87 #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
88
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
89 $header
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
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 -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
92 -l '#echo json.dumps(filename_to_element_identifiers)#'
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
93 #if $esf:
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
94 -e $esf
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
95 #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
96 -t $fit_type
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
97 #if $batch_factors:
17
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
98 --batch_factors '$batch_factors'
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
99 #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
100 #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
101 -a
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
102 #end if
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
103 #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
104 -b
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
105 #end if
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
106 #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
107 -c
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
108 #end if
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
109 #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
110 -m
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
111 #end if
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
112 #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
113 -i
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
114 -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
115 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
116 -x mapping.gff
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
117 #else:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
118 -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
119 #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
120
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
121 #end if
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
122 ]]></command>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
123 <inputs>
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
124 <conditional name="select_data">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
125 <param name="how" type="select">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
126 <option value="datasets_per_level">Select datasets per level</option>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
127 <option value="group_tags">Select group tags corresponding to levels</option>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
128 </param>
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
129 <when value="group_tags">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
130 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
131 <expand macro="factor_repeat">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
132 <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
133 </expand>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
134 </when>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
135 <when value="datasets_per_level">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
136 <expand macro="factor_repeat">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
137 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
138 </expand>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
139 </when>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
140 </conditional>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
141
17
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
142 <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
143 <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
144
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
145 <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
146 <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
147 <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
148 <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
149 </param>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
150 <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
151 <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
152 <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
153 <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
154 <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
155 </param>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
156 <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
157 <param name="mapping_format_selector" type="select" label="Gene mapping format">
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
158 <option value="gtf" selected="True">GTF/GFF3</option>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
159 <option value="tabular">Transcript-ID to Gene-ID mapping file</option>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
160 </param>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
161 <when value="gtf">
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
162 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
163 </when>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
164 <when value="tabular">
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
165 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
166 </when>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
167 </conditional>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
168 </when>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
169 <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
170 </conditional>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
171 <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
172 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
173 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
174 <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
175 label="Output normalized counts table" />
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
176 <param name="normRLog" type="boolean" truevalue="1" falsevalue="0" checked="false"
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
177 label="Output rLog normalized table" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
178 <param name="normVST" type="boolean" truevalue="1" falsevalue="0" checked="false"
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
179 label="Output VST normalized table" />
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
180 <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
181 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
182 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
183 <param name="esf" type="select" label="(Optional) Method for estimateSizeFactors"
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
184 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq.
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
185 The size factor is the median ratio of the sample over a 'pseudosample': for each gene, the geometric mean of all samples.
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
186 'poscounts' and 'iterate' offer alternative estimators, which can be used even when all genes contain a sample with a zero (a problem
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
187 for the default method, as the geometric mean becomes zero, and the ratio undefined). The 'poscounts' estimator deals with a gene with
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
188 some zeros, by calculating a modified geometric mean by taking the n-th root of the product of the non-zero counts. This evolved out of
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
189 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
190 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model.">
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
191 <option value="" selected="true">No Selection (use default)</option>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
192 <option value="ratio">ratio</option>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
193 <option value="poscounts">poscounts</option>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
194 <option value="iterate">iterate</option>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
195 </param>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
196 <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
197 <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
198 <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
199 <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
200 </param>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
201 <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
202 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
203 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
204 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
205 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
206 <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
207 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
208 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
209 filter genes which contain a Cook’s distance above a cutoff" />
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
210 <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
211 label="Turn off independent filtering"
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
212 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
213 </inputs>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
214 <outputs>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
215 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
216 <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
217 <actions>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
218 <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
219 </actions>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
220 </data>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
221 <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
222 <filter>many_contrasts is True</filter>
24
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
223 <discover_datasets pattern="(?P&lt;designation&gt;.+_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
224 </collection>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
225 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
226 <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
227 </data>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
228 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
229 <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
230 </data>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
231 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
232 <filter>normRLog == True</filter>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
233 </data>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
234 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
235 <filter>normVST == True</filter>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
236 </data>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
237 </outputs>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
238 <tests>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
239 <!--Ensure counts files with header works -->
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
240 <test expect_num_outputs="4">
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
241 <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
242 <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
243 <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
244 <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
245 <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
246 </repeat>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
247 <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
248 <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
249 <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
250 </repeat>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
251 </repeat>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
252 <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
253 <param name="normCounts" value="True"/>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
254 <param name="normRLog" value="True"/>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
255 <param name="normVST" 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
256 <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
257 <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
258 <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
259 <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
260 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
261 </output>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
262 <output name="rlog_out">
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
263 <assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
264 <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" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
265 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
266 </assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
267 </output>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
268 <output name="vst_out">
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
269 <assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
270 <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" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
271 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
272 </assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
273 </output>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
274 <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
275 <assert_contents>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
276 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
277 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
278 </output>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
279 </test>
17
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
280 <!--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
281 <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
282 <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
283 <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
284 <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
285 <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
286 <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
287 </repeat>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
288 <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
289 <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
290 <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
291 </repeat>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
292 </repeat>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
293 <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
294 <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
295 <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
296 <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
297 <assert_contents>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
298 <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
299 </assert_contents>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
300 </output>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
301 </test>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
302 <!--Ensure counts files without header works -->
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
303 <test expect_num_outputs="4">
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
304 <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
305 <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
306 <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
307 <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
308 <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
309 </repeat>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
310 <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
311 <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
312 <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
313 </repeat>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
314 </repeat>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
315 <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
316 <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
317 <param name="normCounts" value="True"/>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
318 <param name="normRLog" value="True"/>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
319 <param name="normVST" 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
320 <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
321 <assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
322 <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
323 <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
324 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
325 </output>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
326 <output name="rlog_out">
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
327 <assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
328 <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" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
329 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
330 </assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
331 </output>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
332 <output name="vst_out">
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
333 <assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
334 <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" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
335 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
336 </assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
337 </output>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
338 <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
339 <assert_contents>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
340 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
341 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
342 </output>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
343 </test>
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
344 <!--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
345 <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
346 <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
347 <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
348 <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
349 <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
350 <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
351 </repeat>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
352 <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
353 <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
354 <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
355 </repeat>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
356 </repeat>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
357 <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
358 <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
359 <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
360 <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
361 <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
362 <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
363 <assert_contents>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
364 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
365 </assert_contents>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
366 </output>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
367 </test>
20
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
368 <!--Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works-->
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
369 <test expect_num_outputs="1">
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
370 <repeat name="rep_factorName">
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
371 <param name="factorName" value="Treatment"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
372 <repeat name="rep_factorLevel">
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
373 <param name="factorLevel" value="Treated"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
374 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
375 </repeat>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
376 <repeat name="rep_factorLevel">
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
377 <param name="factorLevel" value="Untreated"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
378 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
379 </repeat>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
380 </repeat>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
381 <param name="pdf" value="False"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
382 <param name="tximport_selector" value="tximport"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
383 <param name="txtype" value="sailfish"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
384 <param name="mapping_format_selector" value="gtf"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
385 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
386 <output name="deseq_out" >
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
387 <assert_contents>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
388 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
389 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
390 </output>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
391 </test>
20
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
392 <!--Ensure Sailfish/Salmon input with GTF annotation from Ensembl works-->
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
393 <test expect_num_outputs="1">
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
394 <repeat name="rep_factorName">
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
395 <param name="factorName" value="Treatment"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
396 <repeat name="rep_factorLevel">
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
397 <param name="factorLevel" value="Treated"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
398 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
399 </repeat>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
400 <repeat name="rep_factorLevel">
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
401 <param name="factorLevel" value="Untreated"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
402 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
403 </repeat>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
404 </repeat>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
405 <param name="pdf" value="False"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
406 <param name="tximport_selector" value="tximport"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
407 <param name="txtype" value="sailfish"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
408 <param name="mapping_format_selector" value="gtf"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
409 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
410 <output name="deseq_out" >
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
411 <assert_contents>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
412 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" />
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
413 </assert_contents>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
414 </output>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
415 </test>
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
416 <!--Ensure group tags can be used to select factor levels -->
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
417 <test expect_num_outputs="1">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
418 <param name="select_data|how" value="group_tags"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
419 <param name="select_data|countsFile">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
420 <collection type="list">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
421 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
422 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
423 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
424 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
425 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
426 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
427 </collection>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
428 </param>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
429 <repeat name="rep_factorName">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
430 <param name="factorName" value="Treatment"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
431 <repeat name="rep_factorLevel">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
432 <param name="factorLevel" value="Treated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
433 <param name="groups" value="primary:treated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
434 </repeat>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
435 <repeat name="rep_factorLevel">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
436 <param name="factorLevel" value="Untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
437 <param name="groups" value="primary:untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
438 </repeat>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
439 </repeat>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
440 <param name="pdf" value="False"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
441 <param name="tximport_selector" value="tximport"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
442 <param name="txtype" value="sailfish"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
443 <param name="mapping_format_selector" value="tabular"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
444 <param name="tabular_file" value="tx2gene.tab"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
445 <output name="deseq_out" >
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
446 <assert_contents>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
447 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
448 </assert_contents>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
449 </output>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
450 </test>
24
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
451 <!--Ensure many_contrasts produces output collection -->
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
452 <test expect_num_outputs="1">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
453 <param name="select_data|how" value="group_tags"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
454 <param name="select_data|countsFile">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
455 <collection type="list">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
456 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
457 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
458 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
459 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
460 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
461 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
462 </collection>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
463 </param>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
464 <repeat name="rep_factorName">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
465 <param name="factorName" value="Treatment"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
466 <repeat name="rep_factorLevel">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
467 <param name="factorLevel" value="Treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
468 <param name="groups" value="primary:treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
469 </repeat>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
470 <repeat name="rep_factorLevel">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
471 <param name="factorLevel" value="Untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
472 <param name="groups" value="primary:untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
473 </repeat>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
474 </repeat>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
475 <param name="pdf" value="False"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
476 <param name="tximport_selector" value="tximport"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
477 <param name="txtype" value="sailfish"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
478 <param name="mapping_format_selector" value="tabular"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
479 <param name="tabular_file" value="tx2gene.tab"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
480 <param name="many_contrasts" value="true"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
481 <output_collection name="split_output" type="list" count="1">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
482 <element name="Treatment_Treated_vs_Untreated">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
483 <assert_contents>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
484 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
485 </assert_contents>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
486 </element>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
487 </output_collection>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
488 </test>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
489 </tests>
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
490 <help><![CDATA[
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
491 .. class:: infomark
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
492
3
248e9c78346e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents: 2
diff changeset
493 **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
494
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
495 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
496
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
497 -----
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
498
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
499 **Inputs**
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
500
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
501 **Count Files**
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
502
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
503 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
504
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
505 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
506
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
507 ========= ============== ===============
3
248e9c78346e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents: 2
diff changeset
508 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
509 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
510 Treatment Treated Untreated
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
511 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
512 Condition Knockdown Wildtype
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
513 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
514 TimePoint Day4 Day1
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
515 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
516 SeqType SingleEnd PairedEnd
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
517 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
518 Gender Female Male
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
519 ========= ============== ===============
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
520
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
521 *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
522
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
523 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
524
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
525 **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
526
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
527 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
528
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
529 Example:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
530
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
531 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
532 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
533 ------------ ---------- --------------- ----------- -----------
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
534 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
535 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
536 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
537 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
538 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
539 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
540 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
541 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
542 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
543 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
544
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
545 **kallisto Files**
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
546
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
547 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
548
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
549 Example:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
550
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
551 ============ ========== =============== =========== ===========
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
552 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
553 ------------ ---------- --------------- ----------- -----------
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
554 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
555 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
556 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
557 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
558 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
559 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
560 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
561 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
562 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
563 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
564
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
565 -----
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
566
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
567 **Output**
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
568
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
569 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
570
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
571 ====== ==========================================================
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
572 Column Description
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
573 ------ ----------------------------------------------------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
574 1 Gene Identifiers
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
575 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
576 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
577 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
578 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
579 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
580 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
581 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
582 ====== ==========================================================
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
583
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
584 .. _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
585 .. _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
586 ]]></help>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
587 <citations>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
588 <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
589 </citations>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
590 </tool>