Mercurial > repos > iuc > ruvseq

annotate ruvseq.xml.orig @ 4:6d7a31ff056f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:22:16 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1 <tool id="ruvseq" name="Remove Unwanted Variation" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
2 <description>from RNA-seq data</description>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
3 <<<<<<< HEAD
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
4 <macros>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
5 <token name="@TOOL_VERSION@">1.16.0</token>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
6 <token name="@WRAPPER_VERSION@">1</token>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
7 </macros>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
8 =======
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
9 <xrefs>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
10 <xref type='bio.tools'>ruvseq</xref>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
11 </xrefs>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
12 >>>>>>> 0851b8679 (add tools up until R)
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
13 <requirements>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
14 <requirement type="package" version="@TOOL_VERSION@">bioconductor-ruvseq</requirement>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
15 <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
16 <requirement type="package" version="1.10.0">bioconductor-tximport</requirement>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
17 <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
18 <requirement type="package" version="0.8.0">r-ggrepel</requirement>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
19 <requirement type="package" version="1.20.2">r-getopt</requirement>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
20 </requirements>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
21 <stdio>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
22 <regex match="Execution halted"
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
23 source="both"
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
24 level="fatal"
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
25 description="Execution halted." />
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
26 <regex match="Error in"
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
27 source="both"
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
28 level="fatal"
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
29 description="An undefined error occurred, please check your input carefully and contact your administrator." />
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
30 <regex match="Fatal error"
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
31 source="both"
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
32 level="fatal"
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
33 description="An undefined error occurred, please check your input carefully and contact your administrator." />
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
34 </stdio>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
35 <version_command><![CDATA[
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
36 echo $(R --version | grep version | grep -v GNU)", RUVSeq version" $(R --vanilla --slave -e "library(RUVSeq); cat(sessionInfo()\$otherPkgs\$RUVSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
37 ]]></version_command>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
38 <command><![CDATA[
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
39 #if $tximport.tximport_selector == 'tximport':
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
40 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
41 ln -s '$tximport.mapping_format.gtf_file' mapping.gtf &&
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
42 #else:
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
43 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
44 #end if
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
45 #end if
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
46
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
47 Rscript '${__tool_directory__}/ruvseq.R'
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
48 #if $pdf:
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
49 -p '$plots'
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
50 #end if
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
51
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
52 --sample_json '$sampleTable'
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
53
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
54 $header
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
55
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
56 --min_k $min_k
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
57 --max_k $max_k
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
58 --min_mean_count $min_mean_count
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
59
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
60 #if $tximport.tximport_selector == 'tximport':
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
61 --txtype $tximport.txtype
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
62 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
63 --tx2gene mapping.gtf
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
64 #else:
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
65 --tx2gene mapping.txt
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
66 #end if
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
67 #end if
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
68 ]]></command>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
69 <configfiles>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
70 <configfile name="sampleTable">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
71 #import json
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
72 #set sample_table = []
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
73 #for $level in $rep_factorLevel:
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
74 #for $file in $level.countsFile:
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
75 #silent $sample_table.append({"path": str($file), "label": str($file.element_identifier), "condition": str($level.factorLevel)})
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
76 #end for
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
77 #end for
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
78 #echo json.dumps($sample_table)
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
79 </configfile>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
80 </configfiles>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
81 <inputs>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
82 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
83 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
84 help="Only letters, numbers and underscores will be retained in this field">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
85 <sanitizer>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
86 <valid initial="string.letters,string.digits"><add value="_" /></valid>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
87 </sanitizer>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
88 </param>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
89 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
90 </repeat>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
91 <param name="min_k" type="integer" value="1" min="1" label="Try to find at least this many factors of unwanted variation" />
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
92 <param name="max_k" type="integer" value="1" min="1" label="Try to find at most this many factors of unwanted variation" />
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
93 <param name="min_mean_count" type="integer" value="5" min="0" label="Ignore genes with fewer than this many counts on average" />
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
94 <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" />
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
95
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
96 <conditional name="tximport">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
97 <param name="tximport_selector" type="select" label="Choice of Input data">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
98 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
99 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
100 </param>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
101 <when value="tximport">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
102 <param name="txtype" type="select" label="Program used to generate TPMs">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
103 <option value="kallisto">kallisto</option>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
104 <option value="sailfish">Sailfish</option>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
105 <option value="salmon">Salmon</option>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
106 </param>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
107 <conditional name="mapping_format">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
108 <param name="mapping_format_selector" type="select" label="Gene mapping format">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
109 <option value="gtf" selected="True">GTF</option>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
110 <option value="tabular">Transcript-ID and Gene-ID mapping file</option>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
111 </param>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
112 <when value="gtf">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
113 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 file with Transcript - Gene mapping"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
114 </when>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
115 <when value="tabular">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
116 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
117 </when>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
118 </conditional>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
119 </when>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
120 <when value="count" />
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
121 </conditional>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
122 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
123 label="Visualising the analysis results"
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
124 help="output an additional PDF files" />
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
125 </inputs>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
126 <outputs>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
127 <collection name="unwanted_variation" type="list" label="RUVSeq covariate files on ${on_string}">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
128 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tabular" format="tabular" directory="." visible="false"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
129 </collection>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
130 <data format="pdf" name="plots" label="RUVSeq diagonstic plots on ${on_string}">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
131 <filter>pdf == True</filter>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
132 </data>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
133 </outputs>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
134 <tests>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
135 <!--Ensure counts files with header works -->
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
136 <test>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
137 <repeat name="rep_factorLevel">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
138 <param name="factorLevel" value="Treated"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
139 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
140 </repeat>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
141 <repeat name="rep_factorLevel">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
142 <param name="factorLevel" value="Untreated"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
143 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
144 </repeat>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
145 <param name="pdf" value="true"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
146 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
147 <output_collection name="unwanted_variation" type="list">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
148 <element name="batch_effects_control_method_k1">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
149 <assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
150 <has_text_matching expression="identifier\tcondition\tW_1"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
151 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
152 </assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
153 </element>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
154 <element name="batch_effects_replicate_method_k1">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
155 <assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
156 <has_text_matching expression="identifier\tcondition\tW_1"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
157 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
158 </assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
159 </element>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
160 <element name="batch_effects_residual_method_k1">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
161 <assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
162 <has_text_matching expression="identifier\tcondition\tW_1"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
163 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
164 </assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
165 </element>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
166 </output_collection>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
167 </test>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
168 <!--Ensure counts files without header works -->
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
169 <test>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
170 <repeat name="rep_factorLevel">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
171 <param name="factorLevel" value="Treated"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
172 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
173 </repeat>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
174 <repeat name="rep_factorLevel">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
175 <param name="factorLevel" value="Untreated"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
176 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
177 </repeat>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
178 <param name="pdf" value="true"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
179 <param name="header" value="false"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
180 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
181 <output_collection name="unwanted_variation" type="list">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
182 <element name="batch_effects_control_method_k1">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
183 <assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
184 <has_text_matching expression="identifier\tcondition\tW_1"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
185 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
186 </assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
187 </element>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
188 <element name="batch_effects_replicate_method_k1">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
189 <assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
190 <has_text_matching expression="identifier\tcondition\tW_1"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
191 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
192 </assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
193 </element>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
194 <element name="batch_effects_residual_method_k1">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
195 <assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
196 <has_text_matching expression="identifier\tcondition\tW_1"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
197 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
198 </assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
199 </element>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
200 </output_collection>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
201 </test>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
202 <!--Ensure sailfish files work -->
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
203 <test>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
204 <repeat name="rep_factorLevel">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
205 <param name="factorLevel" value="Treated"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
206 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
207 </repeat>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
208 <repeat name="rep_factorLevel">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
209 <param name="factorLevel" value="Untreated"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
210 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
211 </repeat>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
212 <param name="pdf" value="true"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
213 <param name="tximport_selector" value="tximport"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
214 <param name="txtype" value="sailfish"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
215 <param name="mapping_format_selector" value="tabular"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
216 <param name="tabular_file" value="tx2gene.tab"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
217 <param name="min_mean_count" value="0"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
218 <output name="plots" file="ruvseq_diag_sailfish.pdf" ftype="pdf" compare="sim_size"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
219 <output_collection name="unwanted_variation" type="list">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
220 <element name="batch_effects_control_method_k1">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
221 <assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
222 <has_text_matching expression="identifier\tcondition\tW_1"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
223 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
224 </assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
225 </element>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
226 <element name="batch_effects_replicate_method_k1">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
227 <assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
228 <has_text_matching expression="identifier\tcondition\tW_1"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
229 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
230 </assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
231 </element>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
232 <element name="batch_effects_residual_method_k1">
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
233 <assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
234 <has_text_matching expression="identifier\tcondition\tW_1"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
235 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
236 </assert_contents>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
237 </element>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
238 </output_collection>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
239 </test>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
240 </tests>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
241 <help><![CDATA[
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
242 .. class:: infomark
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
243
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
244 **What it does**
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
245
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
246 RUVSeq normalizes RNA-seq data using factor analysis of control genes or samples. RUVSeq has been designed for detecting unwanted variation using replicate sample information. The current RUVSeq Galaxy tool only implements estimating unwanted variation for primary factors.
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
247 RUVSeq implements 3 different methods for the estimation of unwanted variation:
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
248
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
249 RUVg estimates the factors of unwanted variation using control genes
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
250
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
251 RUVs estimates the factors of unwanted variation using replicate samples
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
252
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
253 RUVr estimating the factors of unwanted variation using residuals.
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
254
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
255 This tool runs all RUV methods and outputs diagnostic plots and tables with covariates that
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
256 may be used for differential expression analsys.
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
257
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
258 -----
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
259
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
260 **Inputs**
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
261
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
262 **Count Files**
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
263
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
264 RUVSeq_ 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.
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
265
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
266 RUVSeq_ 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.
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
267
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
268 **Salmon or Sailfish Files**
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
269
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
270 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.
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
271
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
272 Example:
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
273
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
274 ============ ========== =============== =========== ===========
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
275 Name Length EffectiveLength TPM NumReads
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
276 ------------ ---------- --------------- ----------- -----------
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
277 NR_001526 164 20.4518 0 0
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
278 NR_001526_1 164 20.4518 0 0
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
279 NR_001526_2 164 20.4518 0 0
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
280 NM_130786 1764 1956.04 2.47415 109.165
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
281 NR_015380 2129 2139.53 1.77331 85.5821
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
282 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
283 NM_001198819 9527 7964.62 0 0
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
284 NM_001198820 9410 7855.78 0 0
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
285 NM_014576 9267 7714.88 0.0481114 8.37255
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
286 ============ ========== =============== =========== ===========
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
287
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
288 **kallisto Files**
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
289
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
290 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below.
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
291
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
292 Example:
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
293
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
294 ============ ========== =============== =========== ===========
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
295 target_id length eff_length est_counts tpm
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
296 ------------ ---------- --------------- ----------- -----------
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
297 NR_001526 164 20.4518 0 0
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
298 NR_001526_1 164 20.4518 0 0
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
299 NR_001526_2 164 20.4518 0 0
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
300 NM_130786 1764 1956.04 109.165 2.47415
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
301 NR_015380 2129 2139.53 85.5821 1.77331
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
302 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
303 NM_001198819 9527 7964.62 0 0
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
304 NM_001198820 9410 7855.78 0 0
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
305 NM_014576 9267 7714.88 8.37255 0.0481114
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
306 ============ ========== =============== =========== ===========
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
307
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
308 -----
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
309
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
310 **Output**
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
311
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
312 RUVSeq_ generates a tabular file for each method and each k of variation as well as a summary PDF.
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
313
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
314 .. _RUVSeq: http://master.bioconductor.org/packages/release/bioc/html/RUVSeq.html
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
315 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
316 ]]></help>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
317 <citations>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
318 <citation type="doi">10.1038/nbt.2931</citation>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
319 </citations>
6d7a31ff056f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
320 </tool>