deseq2: deseq2.xml annotate

annotate deseq2.xml @ 37:951876579237 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"

author	iuc
date	Wed, 25 Nov 2020 18:35:56 +0000
parents	d9f48120c02b
children	cf2c5e8ea088

rev	line source
36 d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	1 <tool id="deseq2" name="DESeq2" version="2.11.40.6+galaxy1">
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	2 <description>Determines differentially expressed features from count tables</description>
34 f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	3 <macros>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	4 <import>deseq2_macros.xml</import>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	5 </macros>
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	6 <requirements>
34 f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	7 <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement>
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	8 <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
34 f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	9 <requirement type="package" version="2.26.2">bioconductor-rhdf5</requirement>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	10 <requirement type="package" version="1.10.0">bioconductor-tximport</requirement>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	11 <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	12 <requirement type="package" version="1.20.2">r-getopt</requirement>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	13 <requirement type="package" version="0.8.0">r-ggrepel</requirement>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	14 <requirement type="package" version="3.0.1">r-gplots</requirement>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	15 <requirement type="package" version="1.0.10">r-pheatmap</requirement>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	16 <requirement type="package" version="0.2.20">r-rjson</requirement>
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	17 </requirements>
6 982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f iuc parents: 5 diff changeset	18 <stdio>
982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f iuc parents: 5 diff changeset	19 <regex match="Execution halted"
982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f iuc parents: 5 diff changeset	20 source="both"
982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f iuc parents: 5 diff changeset	21 level="fatal"
982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f iuc parents: 5 diff changeset	22 description="Execution halted." />
982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f iuc parents: 5 diff changeset	23 <regex match="Error in"
982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f iuc parents: 5 diff changeset	24 source="both"
982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f iuc parents: 5 diff changeset	25 level="fatal"
19 1f88c99898b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82d6e2f33ec7b26276715e01c5b17944a0f5cd0f iuc parents: 18 diff changeset	26 description="An undefined error occurred, please check your input carefully and contact your administrator." />
6 982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f iuc parents: 5 diff changeset	27 <regex match="Fatal error"
982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f iuc parents: 5 diff changeset	28 source="both"
982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f iuc parents: 5 diff changeset	29 level="fatal"
19 1f88c99898b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82d6e2f33ec7b26276715e01c5b17944a0f5cd0f iuc parents: 18 diff changeset	30 description="An undefined error occurred, please check your input carefully and contact your administrator." />
6 982bd8bfa44c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f iuc parents: 5 diff changeset	31 </stdio>
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	32 <version_command><![CDATA[
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	33 echo $(R --version \| grep version \| grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null \| grep -v -i "WARNING: ")
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	34 ]]></version_command>
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	35 <command><![CDATA[
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	36 #if $tximport.tximport_selector == 'tximport':
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	37 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	38 ln -s '$tximport.mapping_format.gtf_file' mapping.gff &&
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	39 #else:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	40 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	41 #end if
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	42 #end if
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	43
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	44 #import json
24 1a34aec44d60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418 iuc parents: 23 diff changeset	45 #import os
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	46 Rscript '${__tool_directory__}/deseq2.R'
33 4f497a8a72e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 05bc13637dc9f8e523bc72844ff6eb0794f98ad3 iuc parents: 32 diff changeset	47 --cores \${GALAXY_SLOTS:-1}
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	48 -o '$deseq_out'
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	49 #if $pdf:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	50 -p '$plots'
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	51 #end if
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	52 #if $normCounts:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	53 -n '$counts_out'
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	54 #end if
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	55 #if $normRLog:
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	56 -r '$rlog_out'
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	57 #end if
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	58 #if $normVST:
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	59 -v '$vst_out'
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	60 #end if
24 1a34aec44d60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418 iuc parents: 23 diff changeset	61 #set $filename_to_element_identifiers = {}
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	62 #set $temp_factor_names = list()
34 f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	63 #for $factor in $select_data.rep_factorName:
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	64 #set $temp_factor = list()
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	65 #for $level in $factor.rep_factorLevel:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	66 #set $count_files = list()
34 f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	67 #if $select_data.how == 'group_tags':
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	68 #for $group in $level.groups.value:
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	69 #for $file in $select_data.countsFile.get_datasets_for_group($group):
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	70 $count_files.append(str($file))
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	71 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	72 #end for
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	73 #end for
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	74 #else:
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	75 #for $file in $level.countsFile:
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	76 $count_files.append(str($file))
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	77 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	78 #end for
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	79 #end if
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	80 $temp_factor.append( {str($level.factorLevel): $count_files} )
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	81 #end for
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	82 $temp_factor.reverse()
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	83 $temp_factor_names.append([str($factor.factorName), $temp_factor])
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	84 #end for
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	85
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	86 $header
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	87
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	88 -f '#echo json.dumps(temp_factor_names)#'
24 1a34aec44d60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418 iuc parents: 23 diff changeset	89 -l '#echo json.dumps(filename_to_element_identifiers)#'
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	90 #if $esf:
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	91 -e $esf
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	92 #end if
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	93 -t $fit_type
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	94 #if $batch_factors:
29 66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	95 --batch_factors '$batch_factors'
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	96 #end if
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	97 #if $outlier_replace_off:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	98 -a
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	99 #end if
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	100 #if $outlier_filter_off:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	101 -b
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	102 #end if
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	103 #if $auto_mean_filter_off:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	104 -c
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	105 #end if
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	106 #if $many_contrasts:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	107 -m
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	108 #end if
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	109 #if $tximport.tximport_selector == 'tximport':
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	110 -i
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	111 -y $tximport.txtype
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	112 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	113 -x mapping.gff
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	114 #else:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	115 -x mapping.txt
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	116 #end if
16 a7bf54ecfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit da90fed6a52526d14b5e58fc3c5e7e8448d783d7 iuc parents: 15 diff changeset	117
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	118 #end if
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	119 ]]></command>
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	120 <inputs>
34 f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	121 <conditional name="select_data">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	122 <param name="how" type="select">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	123 <option value="datasets_per_level">Select datasets per level</option>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	124 <option value="group_tags">Select group tags corresponding to levels</option>
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	125 </param>
34 f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	126 <when value="group_tags">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	127 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	128 <expand macro="factor_repeat">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	129 <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	130 </expand>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	131 </when>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	132 <when value="datasets_per_level">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	133 <expand macro="factor_repeat">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	134 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	135 </expand>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	136 </when>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	137 </conditional>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	138
29 66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	139 <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."/>
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	140 <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" />
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	141
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	142 <conditional name="tximport">
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	143 <param name="tximport_selector" type="select" label="Choice of Input data">
26 47267a044ef1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 25 diff changeset	144 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	145 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	146 </param>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	147 <when value="tximport">
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	148 <param name="txtype" type="select" label="Program used to generate TPMs">
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	149 <option value="kallisto">kallisto</option>
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	150 <option value="sailfish">Sailfish</option>
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	151 <option value="salmon">Salmon</option>
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	152 </param>
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	153 <conditional name="mapping_format">
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	154 <param name="mapping_format_selector" type="select" label="Gene mapping format">
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	155 <option value="gtf" selected="True">GTF/GFF3</option>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	156 <option value="tabular">Transcript-ID to Gene-ID mapping file</option>
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	157 </param>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	158 <when value="gtf">
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	159 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/>
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	160 </when>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	161 <when value="tabular">
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	162 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/>
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	163 </when>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	164 </conditional>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	165 </when>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	166 <when value="count" />
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	167 </conditional>
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	168 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	169 label="Visualising the analysis results"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	170 help="output an additional PDF files" />
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	171 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	172 label="Output normalized counts table" />
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	173 <param name="normRLog" type="boolean" truevalue="1" falsevalue="0" checked="false"
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	174 label="Output rLog normalized table" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	175 <param name="normVST" type="boolean" truevalue="1" falsevalue="0" checked="false"
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	176 label="Output VST normalized table" />
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	177 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	178 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	179 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	180 <param name="esf" type="select" label="(Optional) Method for estimateSizeFactors"
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	181 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq.
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	182 The size factor is the median ratio of the sample over a 'pseudosample': for each gene, the geometric mean of all samples.
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	183 'poscounts' and 'iterate' offer alternative estimators, which can be used even when all genes contain a sample with a zero (a problem
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	184 for the default method, as the geometric mean becomes zero, and the ratio undefined). The 'poscounts' estimator deals with a gene with
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	185 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
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	186 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	187 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model.">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	188 <option value="" selected="true">No Selection (use default)</option>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	189 <option value="ratio">ratio</option>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	190 <option value="poscounts">poscounts</option>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	191 <option value="iterate">iterate</option>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	192 </param>
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	193 <param name="fit_type" type="select" label="Fit type">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	194 <option value="1" selected="true">parametric</option>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	195 <option value="2">local</option>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	196 <option value="3">mean</option>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	197 </param>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	198 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	199 label="Turn off outliers replacement (only affects with >6 replicates)"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	200 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	201 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	202 or normalization factor for that sample" />
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	203 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	204 label="Turn off outliers filtering (only affects with >2 replicates)"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	205 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	206 filter genes which contain a Cook’s distance above a cutoff" />
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	207 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	208 label="Turn off independent filtering"
37 951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b" iuc parents: 36 diff changeset	209 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	210 </inputs>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	211 <outputs>
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	212 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	213 <filter>many_contrasts is False</filter>
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	214 <actions>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	215 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	216 </actions>
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	217 </data>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	218 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	219 <filter>many_contrasts is True</filter>
36 d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	220 <discover_datasets pattern="(?P<designation>.+_vs_.+)" format="tabular" directory="." visible="false"/>
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	221 </collection>
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	222 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	223 <filter>pdf == True</filter>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	224 </data>
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	225 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	226 <filter>normCounts == True</filter>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	227 </data>
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	228 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	229 <filter>normRLog == True</filter>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	230 </data>
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	231 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	232 <filter>normVST == True</filter>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	233 </data>
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	234 </outputs>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	235 <tests>
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	236 <!--Ensure counts files with header works -->
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	237 <test expect_num_outputs="4">
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	238 <repeat name="rep_factorName">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	239 <param name="factorName" value="Treatment"/>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	240 <repeat name="rep_factorLevel">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	241 <param name="factorLevel" value="Treated"/>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	242 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	243 </repeat>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	244 <repeat name="rep_factorLevel">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	245 <param name="factorLevel" value="Untreated"/>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	246 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	247 </repeat>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	248 </repeat>
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	249 <param name="pdf" value="False"/>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	250 <param name="normCounts" value="True"/>
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	251 <param name="normRLog" value="True"/>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	252 <param name="normVST" value="True"/>
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	253 <output name="counts_out">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	254 <assert_contents>
28 5707d3c668d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 81fa5b04b9ba9d4b1b59192af0adb1e1e18ca22b iuc parents: 27 diff changeset	255 <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" />
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	256 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	257 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	258 </output>
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	259 <output name="rlog_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	260 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	261 <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" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	262 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	263 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	264 </output>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	265 <output name="vst_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	266 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	267 <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" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	268 <has_text_matching expression="FBgn0000003\t5.\t5.\t5.\t5.\t5.\t5.\t5.*" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	269 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	270 </output>
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	271 <output name="deseq_out" >
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	272 <assert_contents>
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	273 <has_text_matching expression="FBgn0003360\t1933\.9504.\t-2\.8399.\t0\.1309.\t-21\.68.\t.e-104\t.e-101" />
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	274 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	275 </output>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	276 </test>
29 66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	277 <!--Ensure additional batch factor correction works -->
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	278 <test expect_num_outputs="2">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	279 <repeat name="rep_factorName">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	280 <param name="factorName" value="Treatment"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	281 <repeat name="rep_factorLevel">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	282 <param name="factorLevel" value="Treated"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	283 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	284 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	285 <repeat name="rep_factorLevel">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	286 <param name="factorLevel" value="Untreated"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	287 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	288 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	289 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	290 <param name="batch_factors" value="batch_factors.tab"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	291 <param name="pdf" value="False"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	292 <param name="normCounts" value="True"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	293 <output name="deseq_out">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	294 <assert_contents>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	295 <has_text_matching expression="FBgn0003360\t1933.\t-2.9.\t0.1.\t-26.\t1.-152\t4.-149" />
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	296 </assert_contents>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	297 </output>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8 iuc parents: 28 diff changeset	298 </test>
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	299 <!--Ensure counts files without header works -->
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	300 <test expect_num_outputs="4">
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	301 <repeat name="rep_factorName">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	302 <param name="factorName" value="Treatment"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	303 <repeat name="rep_factorLevel">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	304 <param name="factorLevel" value="Treated"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	305 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	306 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	307 <repeat name="rep_factorLevel">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	308 <param name="factorLevel" value="Untreated"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	309 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	310 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	311 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	312 <param name="header" value="False"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	313 <param name="pdf" value="False"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	314 <param name="normCounts" value="True"/>
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	315 <param name="normRLog" value="True"/>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	316 <param name="normVST" value="True"/>
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	317 <output name="counts_out">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	318 <assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	319 <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" />
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	320 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	321 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	322 </output>
30 3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	323 <output name="rlog_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	324 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	325 <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" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	326 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	327 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	328 </output>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	329 <output name="vst_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	330 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	331 <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" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	332 <has_text_matching expression="FBgn0000003\t5.\t5.\t5.\t5.\t5.\t5.\t5.*" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	333 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2 iuc parents: 29 diff changeset	334 </output>
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	335 <output name="deseq_out" >
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	336 <assert_contents>
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	337 <has_text_matching expression="FBgn0003360\t1933\.9504.\t-2\.8399.\t0\.1309.\t-21\.68.\t.e-104\t.e-101" />
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	338 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	339 </output>
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	340 </test>
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	341 <!--Ensure Sailfish/Salmon input with tx2gene table works-->
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	342 <test expect_num_outputs="1">
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	343 <repeat name="rep_factorName">
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	344 <param name="factorName" value="Treatment"/>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	345 <repeat name="rep_factorLevel">
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	346 <param name="factorLevel" value="Treated"/>
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	347 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	348 </repeat>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	349 <repeat name="rep_factorLevel">
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	350 <param name="factorLevel" value="Untreated"/>
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	351 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
17 24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	352 </repeat>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	353 </repeat>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	354 <param name="pdf" value="False"/>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05 iuc parents: 16 diff changeset	355 <param name="tximport_selector" value="tximport"/>
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	356 <param name="txtype" value="sailfish"/>
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	357 <param name="mapping_format_selector" value="tabular"/>
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	358 <param name="tabular_file" value="tx2gene.tab"/>
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	359 <output name="deseq_out" >
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	360 <assert_contents>
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	361 <has_text_matching expression="UGT3A2\t1.8841.\t-0.1329.\t0.6936.\t-0.1917.\t0.8479.\t0.9999." />
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	362 </assert_contents>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	363 </output>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	364 </test>
32 13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	365 <!--Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works-->
31 7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	366 <test expect_num_outputs="1">
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	367 <repeat name="rep_factorName">
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	368 <param name="factorName" value="Treatment"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	369 <repeat name="rep_factorLevel">
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	370 <param name="factorLevel" value="Treated"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	371 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	372 </repeat>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	373 <repeat name="rep_factorLevel">
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	374 <param name="factorLevel" value="Untreated"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	375 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	376 </repeat>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	377 </repeat>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	378 <param name="pdf" value="False"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	379 <param name="tximport_selector" value="tximport"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	380 <param name="txtype" value="sailfish"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	381 <param name="mapping_format_selector" value="gtf"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	382 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	383 <output name="deseq_out" >
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	384 <assert_contents>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e iuc parents: 30 diff changeset	385 <has_text_matching expression="UGT3A2\t1.8841.\t-0.1329.\t0.6936.\t-0.1917.\t0.8479.\t0.9999." />
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	386 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	387 </output>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	388 </test>
32 13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	389 <!--Ensure Sailfish/Salmon input with GTF annotation from Ensembl works-->
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	390 <test expect_num_outputs="1">
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	391 <repeat name="rep_factorName">
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	392 <param name="factorName" value="Treatment"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	393 <repeat name="rep_factorLevel">
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	394 <param name="factorLevel" value="Treated"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	395 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	396 </repeat>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	397 <repeat name="rep_factorLevel">
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	398 <param name="factorLevel" value="Untreated"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	399 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	400 </repeat>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	401 </repeat>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	402 <param name="pdf" value="False"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	403 <param name="tximport_selector" value="tximport"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	404 <param name="txtype" value="sailfish"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	405 <param name="mapping_format_selector" value="gtf"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	406 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	407 <output name="deseq_out" >
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	408 <assert_contents>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	409 <has_text_matching expression="ENSG00000168671\t1.8841.\t-0.1180.\t0.7429.\t-0.1589.\t0.8737.\t0.9999." />
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	410 </assert_contents>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	411 </output>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459 iuc parents: 31 diff changeset	412 </test>
34 f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	413 <!--Ensure group tags can be used to select factor levels -->
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	414 <test expect_num_outputs="1">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	415 <param name="select_data\|how" value="group_tags"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	416 <param name="select_data\|countsFile">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	417 <collection type="list">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	418 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	419 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	420 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	421 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	422 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	423 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	424 </collection>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	425 </param>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	426 <repeat name="rep_factorName">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	427 <param name="factorName" value="Treatment"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	428 <repeat name="rep_factorLevel">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	429 <param name="factorLevel" value="Treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	430 <param name="groups" value="primary:treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	431 </repeat>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	432 <repeat name="rep_factorLevel">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	433 <param name="factorLevel" value="Untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	434 <param name="groups" value="primary:untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	435 </repeat>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	436 </repeat>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	437 <param name="pdf" value="False"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	438 <param name="tximport_selector" value="tximport"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	439 <param name="txtype" value="sailfish"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	440 <param name="mapping_format_selector" value="tabular"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	441 <param name="tabular_file" value="tx2gene.tab"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	442 <output name="deseq_out" >
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	443 <assert_contents>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	444 <has_text_matching expression="HOXC11\t0.557.\t0.324.\t0.437.\t0.741.\t0.458.\t0.999."/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	445 </assert_contents>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	446 </output>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 iuc parents: 33 diff changeset	447 </test>
36 d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	448 <!--Ensure many_contrasts produces output collection -->
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	449 <test expect_num_outputs="1">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	450 <param name="select_data\|how" value="group_tags"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	451 <param name="select_data\|countsFile">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	452 <collection type="list">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	453 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	454 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	455 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	456 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	457 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	458 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	459 </collection>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	460 </param>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	461 <repeat name="rep_factorName">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	462 <param name="factorName" value="Treatment"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	463 <repeat name="rep_factorLevel">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	464 <param name="factorLevel" value="Treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	465 <param name="groups" value="primary:treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	466 </repeat>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	467 <repeat name="rep_factorLevel">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	468 <param name="factorLevel" value="Untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	469 <param name="groups" value="primary:untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	470 </repeat>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	471 </repeat>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	472 <param name="pdf" value="False"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	473 <param name="tximport_selector" value="tximport"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	474 <param name="txtype" value="sailfish"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	475 <param name="mapping_format_selector" value="tabular"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	476 <param name="tabular_file" value="tx2gene.tab"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	477 <param name="many_contrasts" value="true"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	478 <output_collection name="split_output" type="list" count="1">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	479 <element name="Treatment_Treated_vs_Untreated">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	480 <assert_contents>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	481 <has_text_matching expression="HOXC11\t0.557.\t0.324.\t0.437.\t0.741.\t0.458.\t0.999."/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	482 </assert_contents>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	483 </element>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	484 </output_collection>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a" iuc parents: 34 diff changeset	485 </test>
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	486 </tests>
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	487 <help><![CDATA[
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	488 .. class:: infomark
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	489
15 d856341e03c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: 14 diff changeset	490 What it does
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	491
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	492 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
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	493
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	494 -----
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	495
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	496 Inputs
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	497
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	498 Count Files
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	499
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	500 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 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	501
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	502 The following table gives some examples of factors and their levels:
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	503
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	504 ========= ============== ===============
15 d856341e03c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit dd85747b08272b72c7161de9b18d19598bb49de1 iuc parents: 14 diff changeset	505 Factor Factor level 1 Factor level 2
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	506 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	507 Treatment Treated Untreated
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	508 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	509 Condition Knockdown Wildtype
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	510 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	511 TimePoint Day4 Day1
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	512 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	513 SeqType SingleEnd PairedEnd
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	514 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	515 Gender Female Male
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	516 ========= ============== ===============
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	517
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	518 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.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	519
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	520 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.
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	521
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	522 Salmon or Sailfish Files
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	523
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	524 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.
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	525
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	526 Example:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	527
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	528 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	529 Name Length EffectiveLength TPM NumReads
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	530 ------------ ---------- --------------- ----------- -----------
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	531 NR_001526 164 20.4518 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	532 NR_001526_1 164 20.4518 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	533 NR_001526_2 164 20.4518 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	534 NM_130786 1764 1956.04 2.47415 109.165
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	535 NR_015380 2129 2139.53 1.77331 85.5821
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	536 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	537 NM_001198819 9527 7964.62 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	538 NM_001198820 9410 7855.78 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	539 NM_014576 9267 7714.88 0.0481114 8.37255
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	540 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	541
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	542 kallisto Files
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	543
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	544 kallisto ``abundance.tsv`` files can be imported by setting type to kallisto above. An example of the format is shown below.
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	545
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	546 Example:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	547
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	548 ============ ========== =============== =========== ===========
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	549 target_id length eff_length est_counts tpm
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	550 ------------ ---------- --------------- ----------- -----------
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	551 NR_001526 164 20.4518 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	552 NR_001526_1 164 20.4518 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	553 NR_001526_2 164 20.4518 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	554 NM_130786 1764 1956.04 109.165 2.47415
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	555 NR_015380 2129 2139.53 85.5821 1.77331
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	556 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07
27 dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	557 NM_001198819 9527 7964.62 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	558 NM_001198820 9410 7855.78 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032 iuc parents: 26 diff changeset	559 NM_014576 9267 7714.88 8.37255 0.0481114
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	560 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	561
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	562 -----
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	563
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	564 Output
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	565
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	566 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	567
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	568 ====== ==========================================================
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	569 Column Description
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	570 ------ ----------------------------------------------------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	571 1 Gene Identifiers
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	572 2 mean normalised counts, averaged over all samples from both conditions
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	573 3 the logarithm (to basis 2) of the fold change (See the note in inputs section)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	574 4 standard error estimate for the log2 fold change estimate
13 00ff49f9e750 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd iuc parents: 12 diff changeset	575 5 Wald statistic
00ff49f9e750 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd iuc parents: 12 diff changeset	576 6 p value for the statistical significance of this change
00ff49f9e750 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd iuc parents: 12 diff changeset	577 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	578 which controls false discovery rate (FDR)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	579 ====== ==========================================================
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	580
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	581 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
23 d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	582 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c iuc parents: 22 diff changeset	583 ]]></help>
0 5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	584 <citations>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	585 <citation type="doi">10.1186/s13059-014-0550-8</citation>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	586 </citations>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff iuc parents: diff changeset	587 </tool>

Mercurial > repos > iuc > deseq2

annotate deseq2.xml @ 37:951876579237 draft