Mercurial > repos > iuc > ruvseq
annotate ruvseq.xml @ 4:3a083c78896e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
| author | iuc |
|---|---|
| date | Fri, 21 Apr 2023 14:09:17 +0000 |
| parents | d1f7fa5bb3cb |
| children |
| rev | line source |
|---|---|
|
2
fed9d0350d72
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 4daa375d022673d2437d609b1865b78c64b04415"
iuc
parents:
1
diff
changeset
|
1 <tool id="ruvseq" name="Remove Unwanted Variation" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@"> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
2 <description>from RNA-seq data</description> |
|
4
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
3 <xrefs> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
4 <xref type="bio.tools">ruvseq</xref> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
5 <xref type="bioconductor">ruvseq</xref> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
6 </xrefs> |
|
2
fed9d0350d72
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 4daa375d022673d2437d609b1865b78c64b04415"
iuc
parents:
1
diff
changeset
|
7 <macros> |
|
3
d1f7fa5bb3cb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
|
8 <token name="@TOOL_VERSION@">1.26.0</token> |
|
4
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
9 <token name="@WRAPPER_VERSION@">1</token> |
|
2
fed9d0350d72
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 4daa375d022673d2437d609b1865b78c64b04415"
iuc
parents:
1
diff
changeset
|
10 </macros> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
11 <requirements> |
|
2
fed9d0350d72
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 4daa375d022673d2437d609b1865b78c64b04415"
iuc
parents:
1
diff
changeset
|
12 <requirement type="package" version="@TOOL_VERSION@">bioconductor-ruvseq</requirement> |
|
3
d1f7fa5bb3cb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
|
13 <requirement type="package" version="1.32.0">bioconductor-deseq2</requirement> |
|
d1f7fa5bb3cb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
|
14 <requirement type="package" version="1.20.0">bioconductor-tximport</requirement> |
|
d1f7fa5bb3cb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
|
15 <requirement type="package" version="1.44.0">bioconductor-genomicfeatures</requirement> |
|
d1f7fa5bb3cb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
|
16 <requirement type="package" version="0.9.1">r-ggrepel</requirement> |
|
d1f7fa5bb3cb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
|
17 <requirement type="package" version="1.20.3">r-getopt</requirement> |
|
d1f7fa5bb3cb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
|
18 <requirement type="package" version="1.4.4">r-reshape2</requirement> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
19 </requirements> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
20 <stdio> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
21 <regex match="Execution halted" |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
22 source="both" |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
23 level="fatal" |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
24 description="Execution halted." /> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
25 <regex match="Error in" |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
26 source="both" |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
27 level="fatal" |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
28 description="An undefined error occurred, please check your input carefully and contact your administrator." /> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
29 <regex match="Fatal error" |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
30 source="both" |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
31 level="fatal" |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
32 description="An undefined error occurred, please check your input carefully and contact your administrator." /> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
33 </stdio> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
34 <version_command><![CDATA[ |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
35 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: ") |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
36 ]]></version_command> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
37 <command><![CDATA[ |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
38 #if $tximport.tximport_selector == 'tximport': |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
39 #if $tximport.mapping_format.mapping_format_selector == 'gtf': |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
40 ln -s '$tximport.mapping_format.gtf_file' mapping.gtf && |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
41 #else: |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
42 ln -s '$tximport.mapping_format.tabular_file' mapping.txt && |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
43 #end if |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
44 #end if |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
45 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
46 Rscript '${__tool_directory__}/ruvseq.R' |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
47 #if $pdf: |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
48 -p '$plots' |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
49 #end if |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
50 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
51 --sample_json '$sampleTable' |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
52 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
53 $header |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
54 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
55 --min_k $min_k |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
56 --max_k $max_k |
|
1
c24765926774
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
iuc
parents:
0
diff
changeset
|
57 --min_mean_count $min_mean_count |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
58 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
59 #if $tximport.tximport_selector == 'tximport': |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
60 --txtype $tximport.txtype |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
61 #if $tximport.mapping_format.mapping_format_selector == 'gtf': |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
62 --tx2gene mapping.gtf |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
63 #else: |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
64 --tx2gene mapping.txt |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
65 #end if |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
66 #end if |
|
4
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
67 |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
68 #if $ruv_ncounts == 1: |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
69 --ruv_ncounts |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
70 #end if |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
71 ]]></command> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
72 <configfiles> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
73 <configfile name="sampleTable"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
74 #import json |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
75 #set sample_table = [] |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
76 #for $level in $rep_factorLevel: |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
77 #for $file in $level.countsFile: |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
78 #silent $sample_table.append({"path": str($file), "label": str($file.element_identifier), "condition": str($level.factorLevel)}) |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
79 #end for |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
80 #end for |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
81 #echo json.dumps($sample_table) |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
82 </configfile> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
83 </configfiles> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
84 <inputs> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
85 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
86 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
87 help="Only letters, numbers and underscores will be retained in this field"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
88 <sanitizer> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
89 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
90 </sanitizer> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
91 </param> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
92 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
93 </repeat> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
94 <param name="min_k" type="integer" value="1" min="1" label="Try to find at least this many factors of unwanted variation" /> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
95 <param name="max_k" type="integer" value="1" min="1" label="Try to find at most this many factors of unwanted variation" /> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
96 <param name="min_mean_count" type="integer" value="5" min="0" label="Ignore genes with fewer than this many counts on average" /> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
97 <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" /> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
98 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
99 <conditional name="tximport"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
100 <param name="tximport_selector" type="select" label="Choice of Input data"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
101 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
102 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
103 </param> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
104 <when value="tximport"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
105 <param name="txtype" type="select" label="Program used to generate TPMs"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
106 <option value="kallisto">kallisto</option> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
107 <option value="sailfish">Sailfish</option> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
108 <option value="salmon">Salmon</option> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
109 </param> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
110 <conditional name="mapping_format"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
111 <param name="mapping_format_selector" type="select" label="Gene mapping format"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
112 <option value="gtf" selected="True">GTF</option> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
113 <option value="tabular">Transcript-ID and Gene-ID mapping file</option> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
114 </param> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
115 <when value="gtf"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
116 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 file with Transcript - Gene mapping"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
117 </when> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
118 <when value="tabular"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
119 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
120 </when> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
121 </conditional> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
122 </when> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
123 <when value="count" /> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
124 </conditional> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
125 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true" |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
126 label="Visualising the analysis results" |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
127 help="output an additional PDF files" /> |
|
4
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
128 <param name="ruv_ncounts" type="boolean" truevalue="1" falsevalue="0" checked="false" |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
129 label="Output RUVSeq normalized count tables" |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
130 help="If this option is set to Yes, the tool will generate RUVseq normalized count files. Default: No" /> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
131 </inputs> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
132 <outputs> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
133 <collection name="unwanted_variation" type="list" label="RUVSeq covariate files on ${on_string}"> |
|
4
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
134 <discover_datasets pattern="uv_(?P<designation>.+)\.tabular" format="tabular" directory="." visible="false"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
135 </collection> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
136 <collection name="ruv_normcounts" type="list" label="RUVSeq normalized counts on ${on_string}"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
137 <filter>ruv_ncounts == True</filter> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
138 <discover_datasets pattern="ruv_(?P<designation>.+)\.tabular" format="tabular" directory="." visible="false"/> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
139 </collection> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
140 <data format="pdf" name="plots" label="RUVSeq diagonstic plots on ${on_string}"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
141 <filter>pdf == True</filter> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
142 </data> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
143 </outputs> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
144 <tests> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
145 <!--Ensure counts files with header works --> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
146 <test> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
147 <repeat name="rep_factorLevel"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
148 <param name="factorLevel" value="Treated"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
149 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
150 </repeat> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
151 <repeat name="rep_factorLevel"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
152 <param name="factorLevel" value="Untreated"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
153 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
154 </repeat> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
155 <param name="pdf" value="true"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
156 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
157 <output_collection name="unwanted_variation" type="list"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
158 <element name="batch_effects_control_method_k1"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
159 <assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
160 <has_text_matching expression="identifier\tcondition\tW_1"/> |
|
1
c24765926774
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
iuc
parents:
0
diff
changeset
|
161 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
162 </assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
163 </element> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
164 <element name="batch_effects_replicate_method_k1"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
165 <assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
166 <has_text_matching expression="identifier\tcondition\tW_1"/> |
|
1
c24765926774
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
iuc
parents:
0
diff
changeset
|
167 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
168 </assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
169 </element> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
170 <element name="batch_effects_residual_method_k1"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
171 <assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
172 <has_text_matching expression="identifier\tcondition\tW_1"/> |
|
1
c24765926774
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
iuc
parents:
0
diff
changeset
|
173 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
174 </assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
175 </element> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
176 </output_collection> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
177 </test> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
178 <!--Ensure counts files without header works --> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
179 <test> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
180 <repeat name="rep_factorLevel"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
181 <param name="factorLevel" value="Treated"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
182 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
183 </repeat> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
184 <repeat name="rep_factorLevel"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
185 <param name="factorLevel" value="Untreated"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
186 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
187 </repeat> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
188 <param name="pdf" value="true"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
189 <param name="header" value="false"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
190 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
191 <output_collection name="unwanted_variation" type="list"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
192 <element name="batch_effects_control_method_k1"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
193 <assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
194 <has_text_matching expression="identifier\tcondition\tW_1"/> |
|
1
c24765926774
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
iuc
parents:
0
diff
changeset
|
195 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
196 </assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
197 </element> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
198 <element name="batch_effects_replicate_method_k1"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
199 <assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
200 <has_text_matching expression="identifier\tcondition\tW_1"/> |
|
1
c24765926774
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
iuc
parents:
0
diff
changeset
|
201 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
202 </assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
203 </element> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
204 <element name="batch_effects_residual_method_k1"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
205 <assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
206 <has_text_matching expression="identifier\tcondition\tW_1"/> |
|
1
c24765926774
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
iuc
parents:
0
diff
changeset
|
207 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
208 </assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
209 </element> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
210 </output_collection> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
211 </test> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
212 <!--Ensure sailfish files work --> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
213 <test> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
214 <repeat name="rep_factorLevel"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
215 <param name="factorLevel" value="Treated"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
216 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
217 </repeat> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
218 <repeat name="rep_factorLevel"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
219 <param name="factorLevel" value="Untreated"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
220 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
221 </repeat> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
222 <param name="pdf" value="true"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
223 <param name="tximport_selector" value="tximport"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
224 <param name="txtype" value="sailfish"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
225 <param name="mapping_format_selector" value="tabular"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
226 <param name="tabular_file" value="tx2gene.tab"/> |
|
1
c24765926774
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
iuc
parents:
0
diff
changeset
|
227 <param name="min_mean_count" value="0"/> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
228 <output name="plots" file="ruvseq_diag_sailfish.pdf" ftype="pdf" compare="sim_size"/> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
229 <output_collection name="unwanted_variation" type="list"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
230 <element name="batch_effects_control_method_k1"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
231 <assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
232 <has_text_matching expression="identifier\tcondition\tW_1"/> |
|
1
c24765926774
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
iuc
parents:
0
diff
changeset
|
233 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
234 </assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
235 </element> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
236 <element name="batch_effects_replicate_method_k1"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
237 <assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
238 <has_text_matching expression="identifier\tcondition\tW_1"/> |
|
1
c24765926774
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
iuc
parents:
0
diff
changeset
|
239 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
240 </assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
241 </element> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
242 <element name="batch_effects_residual_method_k1"> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
243 <assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
244 <has_text_matching expression="identifier\tcondition\tW_1"/> |
|
1
c24765926774
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
iuc
parents:
0
diff
changeset
|
245 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
246 </assert_contents> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
247 </element> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
248 </output_collection> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
249 </test> |
|
4
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
250 <!--Ensure Normalized counts files are generated --> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
251 <test> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
252 <repeat name="rep_factorLevel"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
253 <param name="factorLevel" value="Treated"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
254 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
255 </repeat> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
256 <repeat name="rep_factorLevel"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
257 <param name="factorLevel" value="Untreated"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
258 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
259 </repeat> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
260 <param name="pdf" value="true"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
261 <param name="ruv_ncounts" value="true"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
262 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
263 <output_collection name="ruv_normcounts" type="list"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
264 <element name="norm_counts_control_method_k1"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
265 <assert_contents> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
266 <has_text_matching expression="geneID\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\t.+"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
267 </assert_contents> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
268 </element> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
269 <element name="norm_counts_replicate_method_k1"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
270 <assert_contents> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
271 <has_text_matching expression="geneID\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\t.+"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
272 </assert_contents> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
273 </element> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
274 <element name="norm_counts_residual_method_k1"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
275 <assert_contents> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
276 <has_text_matching expression="geneID\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\t.+"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
277 </assert_contents> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
278 </element> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
279 </output_collection> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
280 </test> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
281 <!--Ensure Normalized counts are generated with sailfish files --> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
282 <test> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
283 <repeat name="rep_factorLevel"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
284 <param name="factorLevel" value="Treated"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
285 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
286 </repeat> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
287 <repeat name="rep_factorLevel"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
288 <param name="factorLevel" value="Untreated"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
289 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
290 </repeat> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
291 <param name="pdf" value="true"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
292 <param name="tximport_selector" value="tximport"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
293 <param name="txtype" value="sailfish"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
294 <param name="mapping_format_selector" value="tabular"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
295 <param name="tabular_file" value="tx2gene.tab"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
296 <param name="min_mean_count" value="0"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
297 <param name="ruv_ncounts" value="true"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
298 <output name="plots" file="ruvseq_diag_sailfish.pdf" ftype="pdf" compare="sim_size"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
299 <output_collection name="ruv_normcounts" type="list"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
300 <element name="norm_counts_control_method_k1"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
301 <assert_contents> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
302 <has_text_matching expression="geneID\tsailfish_quant.sf1.tab\tsailfish_quant.sf2.tab\t.+"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
303 </assert_contents> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
304 </element> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
305 <element name="norm_counts_replicate_method_k1"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
306 <assert_contents> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
307 <has_text_matching expression="geneID\tsailfish_quant.sf1.tab\tsailfish_quant.sf2.tab\t.+"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
308 </assert_contents> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
309 </element> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
310 <element name="norm_counts_residual_method_k1"> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
311 <assert_contents> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
312 <has_text_matching expression="geneID\tsailfish_quant.sf1.tab\tsailfish_quant.sf2.tab\t.+"/> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
313 </assert_contents> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
314 </element> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
315 </output_collection> |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
316 </test> |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
317 </tests> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
318 <help><![CDATA[ |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
319 .. class:: infomark |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
320 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
321 **What it does** |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
322 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
323 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. |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
324 RUVSeq implements 3 different methods for the estimation of unwanted variation: |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
325 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
326 RUVg estimates the factors of unwanted variation using control genes |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
327 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
328 RUVs estimates the factors of unwanted variation using replicate samples |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
329 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
330 RUVr estimating the factors of unwanted variation using residuals. |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
331 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
332 This tool runs all RUV methods and outputs diagnostic plots and tables with covariates that |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
333 may be used for differential expression analsys. |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
334 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
335 ----- |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
336 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
337 **Inputs** |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
338 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
339 **Count Files** |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
340 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
341 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. |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
342 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
343 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. |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
344 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
345 **Salmon or Sailfish Files** |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
346 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
347 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. |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
348 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
349 Example: |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
350 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
351 ============ ========== =============== =========== =========== |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
352 Name Length EffectiveLength TPM NumReads |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
353 ------------ ---------- --------------- ----------- ----------- |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
354 NR_001526 164 20.4518 0 0 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
355 NR_001526_1 164 20.4518 0 0 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
356 NR_001526_2 164 20.4518 0 0 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
357 NM_130786 1764 1956.04 2.47415 109.165 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
358 NR_015380 2129 2139.53 1.77331 85.5821 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
359 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
360 NM_001198819 9527 7964.62 0 0 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
361 NM_001198820 9410 7855.78 0 0 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
362 NM_014576 9267 7714.88 0.0481114 8.37255 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
363 ============ ========== =============== =========== =========== |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
364 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
365 **kallisto Files** |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
366 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
367 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below. |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
368 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
369 Example: |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
370 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
371 ============ ========== =============== =========== =========== |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
372 target_id length eff_length est_counts tpm |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
373 ------------ ---------- --------------- ----------- ----------- |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
374 NR_001526 164 20.4518 0 0 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
375 NR_001526_1 164 20.4518 0 0 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
376 NR_001526_2 164 20.4518 0 0 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
377 NM_130786 1764 1956.04 109.165 2.47415 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
378 NR_015380 2129 2139.53 85.5821 1.77331 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
379 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
380 NM_001198819 9527 7964.62 0 0 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
381 NM_001198820 9410 7855.78 0 0 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
382 NM_014576 9267 7714.88 8.37255 0.0481114 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
383 ============ ========== =============== =========== =========== |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
384 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
385 ----- |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
386 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
387 **Output** |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
388 |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
389 RUVSeq_ generates a tabular file for each method and each k of variation as well as a summary PDF. |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
390 |
|
4
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
391 RUVSeq can also generate RUVSeq normalized count tables. However, *these counts should be used only for exploration. It is important that subsequent DE analysis be done on the original counts, as removing the unwanted factors from the counts can also remove part of a factor of interest*. |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
392 |
|
3a083c78896e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
3
diff
changeset
|
393 |
|
0
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
394 .. _RUVSeq: http://master.bioconductor.org/packages/release/bioc/html/RUVSeq.html |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
395 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
396 ]]></help> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
397 <citations> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
398 <citation type="doi">10.1038/nbt.2931</citation> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
399 </citations> |
|
61dffb20b6f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
|
400 </tool> |