Mercurial > repos > iuc > deseq2

annotate deseq2.xml @ 29:cd9874cb9019 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 cbeb1c4c436be04323bd9a809a6393d00b168d07"
author iuc
date Mon, 29 Nov 2021 18:16:48 +0000
parents 7ff33c2d525b
children 8fe98f7094de
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
1 <tool id="deseq2" name="DESeq2" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@">
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>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
6 <expand macro='requirements'/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
7 <expand macro='edam_ontology' />
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
8 <expand macro='xrefs'/>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
9 <stdio>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
10 <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
11 source="both"
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
12 level="fatal"
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
13 description="Execution halted." />
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
14 <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
15 source="both"
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
16 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
17 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
18 <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
19 source="both"
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
20 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
21 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
22 </stdio>
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
23 <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
24 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
25 ]]></version_command>
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
26 <command><![CDATA[
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
27 #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
28 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
29 ln -s '$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
30 #else:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
31 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
32 #end if
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
33 #end if
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
34
26
6a3a025714d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0b502ee6bfa3e861c8678cabfeb670dc8dfe9519"
iuc
parents: 25
diff changeset
35 ## This is needed for Pulsar to transfer the file
6a3a025714d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0b502ee6bfa3e861c8678cabfeb670dc8dfe9519"
iuc
parents: 25
diff changeset
36 cat '$__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
37
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
38 #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
39 #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
40 Rscript '${__tool_directory__}/deseq2.R'
21
a6fc9228e1a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 05bc13637dc9f8e523bc72844ff6eb0794f98ad3
iuc
parents: 20
diff changeset
41 --cores \${GALAXY_SLOTS:-1}
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
42 -o '$deseq_out'
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
43 #if 'pdf' in $output_options.output_selector:
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
44 -p '$plots'
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
45 #end if
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
46 -A $output_options.alpha_ma
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
47 #if 'normCounts' in $output_options.output_selector:
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
48 -n '$counts_out'
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
49 #end if
29
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
50 #if 'sizefactors' in $output_options.output_selector:
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
51 -F '$sizefactors_out'
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
52 #end if
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
53 #if 'normRLog' in $output_options.output_selector:
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
54 -r '$rlog_out'
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
55 #end if
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
56 #if 'normVST' in $output_options.output_selector:
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
57 -v '$vst_out'
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
58 #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
59 #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
60 #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
61 #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
62 #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
63 #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
64 #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
65 #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
66 #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
67 #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
68 $count_files.append(str($file))
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
69 $filename_to_element_identifiers.__setitem__(os.path.basename(str($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
70 #end for
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
71 #end for
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
72 #else:
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
73 #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
74 $count_files.append(str($file))
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
75 $filename_to_element_identifiers.__setitem__(os.path.basename(str($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
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 #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
78 $temp_factor.append( {str($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
79 #end for
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
80 $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
81 $temp_factor_names.append([str($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
82 #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
83
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
84 $header
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
85
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
86 -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
87 -l '#echo json.dumps(filename_to_element_identifiers)#'
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
88 #if $advanced_options.esf:
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
89 -e $advanced_options.esf
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
90 #end if
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
91 -t $advanced_options.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
92 #if $batch_factors:
17
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
93 --batch_factors '$batch_factors'
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
94 #end if
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
95 #if $advanced_options.outlier_replace_off:
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
96 -a
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
97 #end if
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
98 #if $advanced_options.outlier_filter_off:
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
99 -b
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
100 #end if
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
101 #if $advanced_options.auto_mean_filter_off:
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
102 -c
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
103 #end if
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
104 #if 'many_contrasts' in $output_options.output_selector
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
105 -m
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
106 #end if
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
107 #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
108 -i
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
109 -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
110 #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
111 -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
112 #else:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
113 -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
114 #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
115
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
116 #end if
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
117 ]]></command>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
118 <inputs>
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
119 <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
120 <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
121 <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
122 <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
123 </param>
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
124 <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
125 <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
126 <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
127 <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
128 </expand>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
129 </when>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
130 <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
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="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
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 </conditional>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
136
17
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
137 <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
138 <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
139
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
140 <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
141 <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
142 <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
143 <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
144 </param>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
145 <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
146 <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
147 <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
148 <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
149 <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
150 </param>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
151 <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
152 <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
153 <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
154 <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
155 </param>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
156 <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
157 <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
158 </when>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
159 <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
160 <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
161 </when>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
162 </conditional>
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="count" />
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
165 </conditional>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
166 <section name="advanced_options" title="Advanced options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
167 <param name="esf" type="select" label="Method for estimateSizeFactors"
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
168 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq.
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
169 The size factor is the median ratio of the sample over a 'pseudosample': for each gene, the geometric mean of all samples.
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
170 'poscounts' and 'iterate' offer alternative estimators, which can be used even when all genes contain a sample with a zero (a problem
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
171 for the default method, as the geometric mean becomes zero, and the ratio undefined). The 'poscounts' estimator deals with a gene with
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
172 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
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
173 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
174 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model.">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
175 <option value="" selected="true">No Selection (use default)</option>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
176 <option value="ratio">ratio</option>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
177 <option value="poscounts">poscounts</option>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
178 <option value="iterate">iterate</option>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
179 </param>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
180 <param name="fit_type" type="select" label="Fit type">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
181 <option value="1" selected="true">parametric</option>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
182 <option value="2">local</option>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
183 <option value="3">mean</option>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
184 </param>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
185 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
186 label="Turn off outliers replacement (only affects with >6 replicates)"
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
187 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
188 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
189 or normalization factor for that sample" />
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
190 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
191 label="Turn off outliers filtering (only affects with >2 replicates)"
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
192 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
193 filter genes which contain a Cook’s distance above a cutoff" />
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
194 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
195 label="Turn off independent filtering"
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
196 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
197 </section>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
198 <section name="output_options" title="Output options">
28
7ff33c2d525b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"
iuc
parents: 27
diff changeset
199 <param name="output_selector" type="select" multiple="True" optional="true" display="checkboxes" label="Output selector">
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
200 <option value="pdf" selected="True">Generate plots for visualizing the analysis results</option>
29
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
201 <option value="sizefactors" >Output sample size factors</option>
28
7ff33c2d525b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"
iuc
parents: 27
diff changeset
202 <option value="normCounts">Output normalised counts</option>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
203 <option value="normVST">Output VST normalized table</option>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
204 <option value="normRLog">Output rLog normalized table</option>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
205 <option value="many_contrasts">Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)</option>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
206 </param>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
207 <param name="alpha_ma" type="float" min="0" max="0.5" value="0.1" label="Alpha value for MA-plot" help="Default value is 0.1. This option is only meaninful when plots are generated" />
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
208 </section>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
209 </inputs>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
210 <outputs>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
211 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
212 <filter>'many_contrasts' not in output_options['output_selector']</filter>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
213 <actions>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
214 <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
215 </actions>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
216 </data>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
217 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
218 <filter>output_options['output_selector'] and 'many_contrasts' in output_options['output_selector']</filter>
24
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
219 <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
220 </collection>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
221 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
222 <filter>output_options['output_selector'] and 'pdf' in output_options['output_selector']</filter>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
223 </data>
29
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
224 <data name="sizefactors_out" format="tabular" label="Size Factors on ${on_string}">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
225 <filter>output_options['output_selector'] and 'sizefactors' in output_options['output_selector']</filter>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
226 </data>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
227 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
228 <filter>output_options['output_selector'] and 'normCounts' in output_options['output_selector']</filter>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
229 </data>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
230 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
231 <filter>output_options['output_selector'] and 'normRLog' in output_options['output_selector']</filter>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
232 </data>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
233 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
234 <filter>output_options['output_selector'] and 'normVST' in output_options['output_selector']</filter>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
235 </data>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
236 </outputs>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
237 <tests>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
238 <!--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
239 <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
240 <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
241 <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
242 <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
243 <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
244 <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
245 </repeat>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
246 <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
247 <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
248 <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
249 </repeat>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
250 </repeat>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
251 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
252 <param name="output_selector" value="normCounts,normRLog,normVST"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
253 </section>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
254 <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
255 <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
256 <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
257 <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
258 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
259 </output>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
260 <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
261 <assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
262 <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
263 <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
264 </assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
265 </output>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
266 <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
267 <assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
268 <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
269 <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
270 </assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
271 </output>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
272 <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
273 <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
274 <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
275 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
276 </output>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
277 </test>
17
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
278 <!--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
279 <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
280 <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
281 <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
282 <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
283 <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
284 <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
285 </repeat>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
286 <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
287 <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
288 <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
289 </repeat>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
290 </repeat>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
291 <param name="batch_factors" value="batch_factors.tab"/>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
292 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
293 <param name="output_selector" value="normCounts"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
294 </section>
17
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
295 <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
296 <assert_contents>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
297 <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
298 </assert_contents>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
299 </output>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
300 </test>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
301 <!--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
302 <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
303 <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
304 <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
305 <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
306 <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
307 <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
308 </repeat>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
309 <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
310 <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
311 <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
312 </repeat>
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 <param name="header" value="False"/>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
315 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
316 <param name="output_selector" value="normCounts,normRLog,normVST"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
317 </section>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
318 <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
319 <assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
320 <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
321 <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
322 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
323 </output>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
324 <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
325 <assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
326 <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
327 <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
328 </assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
329 </output>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
330 <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
331 <assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
332 <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
333 <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
334 </assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
335 </output>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
336 <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
337 <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
338 <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
339 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
340 </output>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
341 </test>
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
342 <!--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
343 <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
344 <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
345 <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
346 <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
347 <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
348 <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
349 </repeat>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
350 <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
351 <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
352 <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
353 </repeat>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
354 </repeat>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
355 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
356 <param name="output_selector" value=""/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
357 </section>
6
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>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
381 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
382 <param name="output_selector" value=""/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
383 </section>
19
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="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
385 <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
386 <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
387 <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
388 <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
389 <assert_contents>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
390 <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
391 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
392 </output>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
393 </test>
20
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
394 <!--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
395 <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
396 <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
397 <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
398 <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
399 <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
400 <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
401 </repeat>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
402 <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
403 <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
404 <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
405 </repeat>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
406 </repeat>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
407 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
408 <param name="output_selector" value=""/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
409 </section>
20
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
410 <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
411 <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
412 <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
413 <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
414 <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
415 <assert_contents>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
416 <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
417 </assert_contents>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
418 </output>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
419 </test>
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
420 <!--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
421 <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
422 <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
423 <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
424 <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
425 <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
426 <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
427 <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
428 <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
429 <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
430 <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
431 </collection>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
432 </param>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
433 <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
434 <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
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="Treated"/>
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:treated"/>
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 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
440 <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
441 <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
442 </repeat>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
443 </repeat>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
444 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
445 <param name="output_selector" value=""/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
446 </section>
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
447 <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
448 <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
449 <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
450 <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
451 <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
452 <assert_contents>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
453 <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
454 </assert_contents>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
455 </output>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
456 </test>
24
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
457 <!--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
458 <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
459 <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
460 <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
461 <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
462 <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
463 <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
464 <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
465 <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
466 <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
467 <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
468 </collection>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
469 </param>
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_factorName">
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="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
472 <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
473 <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
474 <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
475 </repeat>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
476 <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
477 <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
478 <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
479 </repeat>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
480 </repeat>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
481 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
482 <param name="output_selector" value="many_contrasts"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
483 </section>
24
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
484 <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
485 <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
486 <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
487 <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
488 <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
489 <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
490 <assert_contents>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
491 <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
492 </assert_contents>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
493 </element>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
494 </output_collection>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
495 </test>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
496 <!--Test alpha_ma option-->
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
497 <test expect_num_outputs="1">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
498 <repeat name="rep_factorName">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
499 <param name="factorName" value="Treatment"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
500 <repeat name="rep_factorLevel">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
501 <param name="factorLevel" value="Treated"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
502 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
503 </repeat>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
504 <repeat name="rep_factorLevel">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
505 <param name="factorLevel" value="Untreated"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
506 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
507 </repeat>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
508 </repeat>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
509 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
510 <param name="output_selector" value=""/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
511 <param name="alpha_ma" value="0.05"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
512 </section>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
513 <param name="tximport_selector" value="tximport"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
514 <param name="txtype" value="sailfish"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
515 <param name="mapping_format_selector" value="gtf"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
516 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
517 <output name="deseq_out" >
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
518 <assert_contents>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
519 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" />
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
520 </assert_contents>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
521 </output>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
522 </test>
29
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
523 <!-- Same as above alpha_ma test, but with size factors -->
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
524 <test expect_num_outputs="2">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
525 <repeat name="rep_factorName">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
526 <param name="factorName" value="Treatment"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
527 <repeat name="rep_factorLevel">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
528 <param name="factorLevel" value="Treated"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
529 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
530 </repeat>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
531 <repeat name="rep_factorLevel">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
532 <param name="factorLevel" value="Untreated"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
533 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
534 </repeat>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
535 </repeat>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
536 <section name="output_options">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
537 <param name="output_selector" value="sizefactors"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
538 <param name="alpha_ma" value="0.05"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
539 </section>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
540 <param name="tximport_selector" value="tximport"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
541 <param name="txtype" value="sailfish"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
542 <param name="mapping_format_selector" value="gtf"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
543 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
544 <output name="sizefactors_out">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
545 <assert_contents>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
546 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+" />
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
547 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+" />
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
548 </assert_contents>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
549 </output>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
550 </test>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
551 <!-- Same as above alpha_ma size factor test, but with a non-default estimator-->
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
552 <test expect_num_outputs="2">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
553 <repeat name="rep_factorName">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
554 <param name="factorName" value="Treatment"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
555 <repeat name="rep_factorLevel">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
556 <param name="factorLevel" value="Treated"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
557 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
558 </repeat>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
559 <repeat name="rep_factorLevel">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
560 <param name="factorLevel" value="Untreated"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
561 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
562 </repeat>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
563 </repeat>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
564 <section name="advanced_options">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
565 <param name="esf" value="poscounts" />
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
566 </section>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
567 <section name="output_options">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
568 <param name="output_selector" value="sizefactors"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
569 <param name="alpha_ma" value="0.05"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
570 </section>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
571 <param name="tximport_selector" value="tximport"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
572 <param name="txtype" value="sailfish"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
573 <param name="mapping_format_selector" value="gtf"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
574 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
575 <output name="sizefactors_out" >
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
576 <assert_contents>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
577 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+" />
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
578 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+" />
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
579 </assert_contents>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
580 </output>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
581 </test>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
582 </tests>
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
583 <help><![CDATA[
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
584 .. class:: infomark
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
585
3
248e9c78346e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents: 2
diff changeset
586 **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
587
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
588 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
589
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
590 -----
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
591
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
592 **Inputs**
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
593
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
594 **Count Files**
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
595
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
596 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
597
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
598 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
599
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
600 ========= ============== ===============
3
248e9c78346e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit f33b04533bca91242b8a0a4077e1d593f5a874e0
iuc
parents: 2
diff changeset
601 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
602 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
603 Treatment Treated Untreated
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
604 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
605 Condition Knockdown Wildtype
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
606 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
607 TimePoint Day4 Day1
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
608 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
609 SeqType SingleEnd PairedEnd
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
610 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
611 Gender Female Male
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
612 ========= ============== ===============
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
613
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
614 *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
615
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
616 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
617
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
618 **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
619
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
620 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
621
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
622 Example:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
623
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
624 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
625 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
626 ------------ ---------- --------------- ----------- -----------
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
627 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
628 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
629 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
630 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
631 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
632 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
633 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
634 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
635 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
636 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
637
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
638 **kallisto Files**
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
639
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
640 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
641
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
642 Example:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
643
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
644 ============ ========== =============== =========== ===========
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
645 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
646 ------------ ---------- --------------- ----------- -----------
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
647 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
648 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
649 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
650 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
651 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
652 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
653 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
654 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
655 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
656 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
657
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
658 -----
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
659
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
660 **Output**
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
661
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
662 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
663
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
664 ====== ==========================================================
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
665 Column Description
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
666 ------ ----------------------------------------------------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
667 1 Gene Identifiers
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
668 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
669 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
670 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
671 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
672 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
673 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
674 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
675 ====== ==========================================================
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
676
29
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
677 By selecting ``Output sample size factors`` in the "Output options"
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
678 selection box, the size factors used to normalize the samples can also
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
679 be output as a tabular file.
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
680
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
681 .. _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
682 .. _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
683 ]]></help>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
684 <expand macro="citations" />
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
685 </tool>