Mercurial > repos > iuc > goseq
annotate goseq.xml.orig @ 9:11385d227014 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
|---|---|
| date | Tue, 31 Aug 2021 08:37:03 +0000 |
| parents | |
| children |
| rev | line source |
|---|---|
|
9
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
1 <tool id="goseq" name="goseq" version="@VERSION@+@GALAXY_VERSION@"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
2 <description>tests for overrepresented gene categories</description> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
3 <xrefs> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
4 <<<<<<< HEAD |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
5 <xref type="bio.tools">goseq</xref> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
6 </xrefs> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
7 <edam_topics> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
8 <edam_topic>topic_3308</edam_topic> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
9 </edam_topics> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
10 <edam_operations> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
11 <edam_operation>operation_2436</edam_operation> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
12 </edam_operations> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
13 ======= |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
14 <xref type='bio.tools'>goseq</xref> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
15 </xrefs> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
16 >>>>>>> c37d72558 (add more bio.tool IDs) |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
17 <macros> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
18 <token name="@VERSION@">1.44.0</token> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
19 <token name="@GALAXY_VERSION@">galaxy0</token> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
20 </macros> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
21 <requirements> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
22 <requirement type="package" version="@VERSION@">bioconductor-goseq</requirement> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
23 <requirement type="package" version="3.13.0">bioconductor-org.hs.eg.db</requirement> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
24 <requirement type="package" version="3.13.0">bioconductor-org.dm.eg.db</requirement> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
25 <requirement type="package" version="3.13.0">bioconductor-org.dr.eg.db</requirement> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
26 <requirement type="package" version="3.13.0">bioconductor-org.mm.eg.db</requirement> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
27 <requirement type="package" version="1.0.6">r-dplyr</requirement> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
28 <requirement type="package" version="3.3.3">r-ggplot2</requirement> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
29 <requirement type="package" version="1.6.6">r-optparse</requirement> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
30 </requirements> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
31 <stdio> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
32 <regex match="Execution halted" |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
33 source="both" |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
34 level="fatal" |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
35 description="Execution halted." /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
36 <regex match="Error in" |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
37 source="both" |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
38 level="fatal" |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
39 description="An undefined error occured, please check your input carefully and contact your administrator." /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
40 <regex match="Fatal error" |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
41 source="both" |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
42 level="fatal" |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
43 description="An undefined error occured, please check your input carefully and contact your administrator." /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
44 </stdio> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
45 <version_command><![CDATA[ |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
46 echo $(R --version | grep version | grep -v GNU)", goseq version" $(R --vanilla --slave -e "library(goseq); cat(sessionInfo()\$otherPkgs\$goseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", dplyr version" $(R --vanilla --slave -e "library(dplyr); cat(sessionInfo()\$otherPkgs\$dplyr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
47 ]]></version_command> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
48 <command><![CDATA[ |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
49 Rscript '$__tool_directory__/goseq.r' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
50 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
51 --dge_file '$dge_file' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
52 --length_file '$length_file' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
53 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
54 #if $categorySource.catSource == 'getgo' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
55 --genome $categorySource.genome |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
56 --gene_id $categorySource.gene_id |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
57 --fetch_cats '$categorySource.fetchcats' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
58 #elif $categorySource.catSource == 'history' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
59 --category_file '$categorySource.category_file' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
60 #end if |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
61 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
62 #if $methods.wallenius |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
63 --wallenius_tab '$wallenius_tab' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
64 #end if |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
65 #if $methods.hypergeometric |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
66 --nobias_tab '$nobias_tab' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
67 #end if |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
68 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
69 --repcnt $methods.repcnt |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
70 #if $methods.repcnt != 0 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
71 --sampling_tab '$sampling_tab' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
72 #end if |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
73 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
74 --p_adj_method '$adv.p_adj_method' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
75 --use_genes_without_cat '$adv.use_genes_without_cat' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
76 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
77 #if $out.topgo_plot |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
78 --top_plot '$top_plot' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
79 #end if |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
80 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
81 #if str($out.make_plots) == 'TRUE' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
82 --make_plots '$out.make_plots' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
83 --length_bias_plot '$length_bias_plot' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
84 #if $methods.repcnt != 0 and $methods.wallenius |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
85 --sample_vs_wallenius_plot '$sample_vs_wallenius_plot' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
86 #end if |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
87 #end if |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
88 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
89 #if $out.cat_genes |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
90 --categories_genes_out_fp '$cat_genes_tab' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
91 #end if |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
92 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
93 #if $out.rdata_out |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
94 --rdata '$rdata' |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
95 #end if |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
96 ]]></command> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
97 <inputs> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
98 <!-- Input Files--> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
99 <param name="dge_file" type="data" format="tabular" label="Differentially expressed genes file" help="A tabular file with Gene IDs in the first column, and True or False in the second column. True means a gene is differentially expressed. See Help section for details."/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
100 <param name="length_file" type="data" format="tabular" label="Gene lengths file" help="You can calculate the gene lengths using featureCounts or the Gene length and GC content tool."/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
101 <conditional name="categorySource"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
102 <param name="catSource" type="select" format="tabular" label="Gene categories" help="You can obtain a mapping of genes to categories (for some genomes only) or you can provide your own category file."> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
103 <option value="getgo" selected="true">Get categories</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
104 <option value="history">Use a category file from history</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
105 </param> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
106 <when value="getgo"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
107 <param name="genome" type="select" label="Select a genome to use"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
108 <option value="hg38">Human (hg38)</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
109 <option value="mm10">Mouse (mm10)</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
110 <option value="dm6">Fruit fly (dm6)</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
111 <option value="danRer10">Zebrafish (danRer10)</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
112 </param> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
113 <param name="gene_id" type="select" label="Select Gene ID format" help="Supported Gene IDs to automatically fetch categories should either be Entrez, Ensembl, or gene symbols."> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
114 <option value="ensGene">Ensembl Gene ID</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
115 <option value="knownGene">Entrez Gene ID</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
116 <option value="geneSymbol">Gene Symbol</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
117 </param> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
118 <param name="fetchcats" type="select" multiple="True" display="checkboxes" label="Select one or more categories" help="By default, goseq tests all three major Gene Ontology branches; Cellular Component, Biological Process and Molecular Function. However, it is possible to limit testing to any combination and/or to also use KEGG pathways."> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
119 <option value="GO:CC" selected="True">GO: Cellular Component</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
120 <option value="GO:BP" selected="True">GO: Biological Process</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
121 <option value="GO:MF" selected="True">GO: Molecular Function</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
122 <option value="KEGG">KEGG</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
123 </param> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
124 </when> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
125 <when value="history"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
126 <param name="category_file" type="data" format="tabular" label="Gene category file"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
127 </when> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
128 </conditional> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
129 <!-- Method Options --> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
130 <section name="methods" title="Method Options"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
131 <param name="wallenius" type="boolean" checked="true" label="Use Wallenius method" help="See help for details" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
132 <param name="hypergeometric" type="boolean" checked="false" label="Use Hypergeometric method" help="Does not use gene length information. See help for details" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
133 <param name="repcnt" type="integer" size="3" min="0" max="10000" value="0" label="Sampling number" help="Number of random samples to be calculated when sampling is used. Set to 0 to not do sampling. Larger values take a long time" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
134 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
135 <!-- Advanced Options --> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
136 <section name="adv" title="Advanced Options"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
137 <param name="p_adj_method" type="select" label="Select a method for multiple hypothesis testing correction"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
138 <option value="BH" selected="True">Benjamini-Hochberg [FDR] (1995)</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
139 <option value="holm">Holm (1979)</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
140 <option value="hommel">Hommel (1988)</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
141 <option value="hochberg">Hochberg (1988)</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
142 <option value="bonferroni">Bonferroni</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
143 <option value="BY">Benjamini - Yekutieli (2001)</option> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
144 </param> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
145 <param name="use_genes_without_cat" type="boolean" checked="false" label="Count genes without any category?" help="For example, a large number of genes may have no GO term annotated. If this option is set to No, those genes will be ignored in the calculation of p-values. If this option is set to Yes, then these genes will count towards the total number of genes outside the category being tested. This was the default behaviour for version 1.15.1 and earlier"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
146 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
147 <!-- Output Options --> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
148 <section name="out" title="Output Options"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
149 <param name="topgo_plot" type="boolean" checked="false" label="Output Top GO terms plot?" help="Output a PDF plot of the Top 10 over-represented GO terms" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
150 <param name="make_plots" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Produce diagnostic plots?" help="This will produce the length bias (PWF) plot. If both sampling and wallenius methods are selected, it will also produce a plot comparing their p-values. These plots may help you compare the different p-value estimation methods that goseq can use" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
151 <param name="cat_genes" type="boolean" checked="false" label="Extract the DE genes for the categories (GO/KEGG terms)?" help="" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
152 <param name="rdata_out" type="boolean" checked="false" label="Output RData file?" help="Output all the data used by R to construct the tables and plots, can be loaded into R" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
153 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
154 </inputs> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
155 <outputs> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
156 <data name="wallenius_tab" format="tabular" label="${tool.name} on ${on_string}: Ranked category list - Wallenius method"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
157 <filter>methods['wallenius']</filter> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
158 </data> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
159 <data name="sampling_tab" format="tabular" label="${tool.name} on ${on_string}: Ranked category list - Sampling method"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
160 <filter>methods['repcnt'] != 0</filter> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
161 </data> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
162 <data name="nobias_tab" format="tabular" label="${tool.name} on ${on_string}: Ranked category list - Hypergeometric method"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
163 <filter>methods['hypergeometric']</filter> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
164 </data> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
165 <data name="length_bias_plot" format="pdf" label="${tool.name} on ${on_string}: Length bias plot"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
166 <filter>out['make_plots']</filter> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
167 </data> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
168 <data name="sample_vs_wallenius_plot" format="pdf" label="${tool.name} on ${on_string}: Sampling vs Wallenius P-values plot"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
169 <filter>methods['repcnt'] != 0</filter> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
170 <filter>methods['wallenius']</filter> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
171 <filter>out['make_plots']</filter> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
172 </data> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
173 <data name="top_plot" format="pdf" label="${tool.name} on ${on_string}: Top over-represented GO terms plot"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
174 <filter>methods['wallenius']</filter> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
175 <filter>out['topgo_plot']</filter> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
176 </data> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
177 <data name="cat_genes_tab" format="tabular" label="${tool.name} on ${on_string}: DE genes for categories (GO/KEGG terms)"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
178 <filter>out['cat_genes']</filter> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
179 </data> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
180 <data name="rdata" format="rdata" label="${tool.name} on ${on_string}: RData file"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
181 <filter>out['rdata_out']</filter> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
182 </data> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
183 </outputs> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
184 <tests> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
185 <!-- Ensure top plot is output and check Wallenius --> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
186 <test expect_num_outputs="2"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
187 <param name="dge_file" value="dge_list.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
188 <param name="length_file" value="gene_length.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
189 <conditional name="categorySource"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
190 <param name="catSource" value="history" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
191 <param name="category_file" value="category.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
192 </conditional> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
193 <section name="methods"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
194 <param name="wallenius" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
195 <param name="hypergeometric" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
196 <param name="repcnt" value="0"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
197 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
198 <section name="adv"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
199 <param name="p_adj_method" value="BH"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
200 <param name="use_genes_without_cat" value="true" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
201 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
202 <section name="out"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
203 <param name="topgo_plot" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
204 <param name="make_plots" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
205 <param name="cat_genes" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
206 <param name="rdata_out" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
207 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
208 <output name="top_plot" ftype="pdf" file="topgo.pdf" compare="sim_size"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
209 <output name="wallenius_tab"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
210 <assert_contents> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
211 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
212 <has_text_matching expression="GO:0000278.*0.01" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
213 </assert_contents> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
214 </output> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
215 </test> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
216 <!-- Ensure getting GO categories works & also DE genes for GO terms--> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
217 <test expect_num_outputs="2"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
218 <param name="dge_file" value="dge_list.tab" ftype="tabular"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
219 <param name="length_file" value="gene_length.tab" ftype="tabular"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
220 <conditional name="categorySource"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
221 <param name="catSource" value="getgo" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
222 <param name="genome" value="hg38" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
223 <param name="gene_id" value="ensGene" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
224 <param name="fetchcats" value="GO:CC,GO:BP,GO:MF"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
225 </conditional> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
226 <section name="methods"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
227 <param name="wallenius" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
228 <param name="hypergeometric" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
229 <param name="repcnt" value="0"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
230 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
231 <section name="adv"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
232 <param name="p_adj_method" value="BH"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
233 <param name="use_genes_without_cat" value="true" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
234 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
235 <section name="out"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
236 <param name="topgo_plot" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
237 <param name="make_plots" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
238 <param name="cat_genes" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
239 <param name="rdata_out" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
240 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
241 <output name="wallenius_tab"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
242 <assert_contents> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
243 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
244 <has_text_matching expression="GO:0005576.*0.9" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
245 </assert_contents> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
246 </output> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
247 <output name="cat_genes_tab"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
248 <assert_contents> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
249 <has_text_matching expression="category.*de_genes" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
250 <has_text_matching expression="GO:0005615.*ENSG00000090402,ENSG00000108953,ENSG00000070961" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
251 </assert_contents> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
252 </output> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
253 </test> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
254 <!-- Ensure getting GO categories for another genome (zebrafish) works --> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
255 <test expect_num_outputs="1"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
256 <param name="dge_file" value="dge_list_zf.tab" ftype="tabular"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
257 <param name="length_file" value="gene_length_zf.tab" ftype="tabular"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
258 <conditional name="categorySource"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
259 <param name="catSource" value="getgo" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
260 <param name="genome" value="danRer10"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
261 <param name="gene_id" value="ensGene" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
262 <param name="fetchcats" value="GO:CC,GO:BP,GO:MF"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
263 </conditional> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
264 <section name="methods"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
265 <param name="wallenius" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
266 <param name="hypergeometric" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
267 <param name="repcnt" value="0"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
268 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
269 <section name="adv"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
270 <param name="p_adj_method" value="BH"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
271 <param name="use_genes_without_cat" value="true" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
272 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
273 <section name="out"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
274 <param name="topgo_plot" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
275 <param name="make_plots" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
276 <param name="cat_genes" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
277 <param name="rdata_out" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
278 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
279 <output name="wallenius_tab"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
280 <assert_contents> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
281 <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
282 <has_text_matching expression="GO:0016569.*0.90" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
283 </assert_contents> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
284 </output> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
285 </test> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
286 <!-- Ensure length bias plot works --> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
287 <test expect_num_outputs="2"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
288 <param name="dge_file" value="dge_list.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
289 <param name="length_file" value="gene_length.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
290 <conditional name="categorySource"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
291 <param name="catSource" value="history" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
292 <param name="category_file" value="category.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
293 </conditional> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
294 <section name="methods"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
295 <param name="wallenius" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
296 <param name="hypergeometric" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
297 <param name="repcnt" value="0"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
298 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
299 <section name="adv"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
300 <param name="p_adj_method" value="BH"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
301 <param name="use_genes_without_cat" value="true" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
302 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
303 <section name="out"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
304 <param name="topgo_plot" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
305 <param name="make_plots" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
306 <param name="cat_genes" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
307 <param name="rdata_out" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
308 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
309 <param name="make_plots" value="true" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
310 <output name="length_bias_plot" ftype="pdf" file="length_bias_plot.pdf" compare="sim_size" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
311 </test> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
312 <!-- Ensure hypergeometric works --> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
313 <test expect_num_outputs="2"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
314 <param name="dge_file" value="dge_list.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
315 <param name="length_file" value="gene_length.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
316 <conditional name="categorySource"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
317 <param name="catSource" value="history" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
318 <param name="category_file" value="category.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
319 </conditional> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
320 <section name="methods"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
321 <param name="wallenius" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
322 <param name="hypergeometric" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
323 <param name="repcnt" value="0"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
324 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
325 <section name="adv"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
326 <param name="p_adj_method" value="BH"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
327 <param name="use_genes_without_cat" value="true" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
328 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
329 <section name="out"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
330 <param name="topgo_plot" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
331 <param name="make_plots" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
332 <param name="cat_genes" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
333 <param name="rdata_out" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
334 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
335 <output name="nobias_tab" file="nobias.tab" compare="contains" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
336 </test> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
337 <!-- Ensure sampling vs wallenius works --> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
338 <test expect_num_outputs="4"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
339 <param name="dge_file" value="dge_list.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
340 <param name="length_file" value="gene_length.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
341 <conditional name="categorySource"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
342 <param name="catSource" value="history" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
343 <param name="category_file" value="category.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
344 </conditional> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
345 <section name="methods"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
346 <param name="wallenius" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
347 <param name="hypergeometric" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
348 <param name="repcnt" value="1000"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
349 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
350 <section name="adv"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
351 <param name="p_adj_method" value="BH"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
352 <param name="use_genes_without_cat" value="true" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
353 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
354 <section name="out"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
355 <param name="topgo_plot" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
356 <param name="make_plots" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
357 <param name="cat_genes" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
358 <param name="rdata_out" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
359 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
360 <output name="sampling_tab" file="samp.tab" compare="sim_size" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
361 <output name="length_bias_plot" ftype="pdf" file="length_bias_plot.pdf" compare="sim_size" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
362 <output name="sample_vs_wallenius_plot" ftype="pdf" file="sample_vs_wallenius_plot.pdf" compare="sim_size" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
363 </test> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
364 <!-- Ensure RData output works --> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
365 <test expect_num_outputs="2"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
366 <param name="dge_file" value="dge_list.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
367 <param name="length_file" value="gene_length.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
368 <conditional name="categorySource"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
369 <param name="catSource" value="history" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
370 <param name="category_file" value="category.tab" ftype="tabular" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
371 </conditional> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
372 <section name="methods"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
373 <param name="wallenius" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
374 <param name="hypergeometric" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
375 <param name="repcnt" value="0"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
376 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
377 <section name="adv"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
378 <param name="p_adj_method" value="BH"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
379 <param name="use_genes_without_cat" value="true" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
380 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
381 <section name="out"> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
382 <param name="topgo_plot" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
383 <param name="make_plots" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
384 <param name="cat_genes" value="false"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
385 <param name="rdata_out" value="true"/> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
386 </section> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
387 <output name="rdata" file="goseq_analysis.RData" compare="sim_size" /> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
388 </test> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
389 </tests> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
390 <help><![CDATA[ |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
391 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
392 .. class:: infomark |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
393 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
394 **What it does** |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
395 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
396 `Gene Ontology`_ (GO) analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but standard methods give biased results on RNA-seq data due to over-detection of differential expression for long and highly expressed transcripts. This tool provides methods for performing GO analysis of RNA-seq data, taking length bias into account. The methods and software used by goseq are equally applicable to other category based tests of RNA-seq data, such as KEGG_ pathway analysis. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
397 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
398 Options map closely to the excellent goseq manual_. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
399 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
400 ----- |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
401 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
402 **Inputs** |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
403 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
404 *Differentially expressed genes file* |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
405 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
406 goseq needs a tabular file containing information on differentially expressed genes. This should contain all genes assayed in the RNA-seq experiment. The file should have two columns with an optional header row. The first column should contain the Gene IDs, which must be unique within the file and not repeated. The second column should contain True or False. True means the gene should count as differentially expressed, False means it is not differentially expressed. You can use the "Compute an expression on every row" tool to create a True / False column for your dataset. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
407 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
408 Example: |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
409 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
410 =============== ===== |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
411 ENSG00000236824 False |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
412 ENSG00000162526 False |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
413 ENSG00000090402 True |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
414 ENSG00000169188 False |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
415 ENSG00000124103 False |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
416 =============== ===== |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
417 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
418 *Gene lengths file* |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
419 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
420 goseq needs information about the length of a gene to correct for potential length bias in differentially expressed genes using a Probability Weight Function (PWF). The PWF can be thought of, as a function which gives the probability that a gene will be differentially expressed, based on its length alone. The gene length file should have two columns with an optional header row. The first column should contain the Gene IDs, and the second column should contain the gene length in bp. If length data is unavailable for some genes, that entry should be set to NA. The goseq authors recommend using the gene lengths obtained from upstream summarization programs, such as **featureCounts**, if provided. Alternatively, the **Gene length and GC content** tool can produce such a file. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
421 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
422 Example: |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
423 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
424 =============== ===== |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
425 ENSG00000236824 13458 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
426 ENSG00000162526 2191 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
427 ENSG00000090402 6138 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
428 ENSG00000169188 3245 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
429 ENSG00000124103 1137 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
430 =============== ===== |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
431 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
432 *Gene categories file* |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
433 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
434 This tool can get GO and KEGG categories for some genomes. The three GO categories are GO:MF (Molecular Function - molecular activities of gene products), GO:CC (Cellular Component - where gene products are active), GO:BP (Biological Process - pathways and larger processes made up of the activities of multiple gene products). If your genome is not available, you will also need a file describing the membership of genes in categories. The category file should have two columns with an optional header row. with Gene ID in the first column and category identifier in the second column. As the mapping between categories and genes is usually many-to-many, this table will usually have multiple rows with the same Gene ID and category identifier. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
435 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
436 Example: |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
437 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
438 =============== =========== |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
439 ENSG00000162526 GO\:0000003 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
440 ENSG00000198648 GO\:0000278 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
441 ENSG00000112312 GO\:0000278 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
442 ENSG00000174442 GO\:0000278 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
443 ENSG00000108953 GO\:0000278 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
444 =============== =========== |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
445 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
446 ----- |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
447 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
448 **Outputs** |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
449 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
450 This tool outputs a tabular file containing a ranked list of gene categories, similar to below. The default output is the Wallenius method table. If the Sampling and/or Hypergeometric methods are also selected, additional tables are produced. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
451 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
452 Example: |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
453 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
454 =========== =============== ================ ============ ========== ======================================== ========== =================== ==================== |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
455 *category* *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term* *ontology* *p_adjust_over_rep* *p_adjust_under_rep* |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
456 ----------- --------------- ---------------- ------------ ---------- ---------------------------------------- ---------- ------------------- -------------------- |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
457 GO\:0005576 0.000054 0.999975 56 142 extracellular region CC 0.394825 1 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
458 GO\:0005840 0.000143 0.999988 9 12 ribosome CC 0.394825 1 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
459 GO\:0044763 0.000252 0.999858 148 473 single-organism cellular process BP 0.394825 1 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
460 GO\:0044699 0.000279 0.999844 158 513 single-organism process BP 0.394825 1 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
461 GO\:0065010 0.000428 0.999808 43 108 extracellular membrane-bounded organelle CC 0.394825 1 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
462 GO\:0070062 0.000428 0.999808 43 108 extracellular exosome CC 0.394825 1 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
463 =========== =============== ================ ============ ========== ======================================== ========== =================== ==================== |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
464 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
465 Optionally, this tool can also output: |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
466 * a plot of the top 10 over-represented GO categories |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
467 * some diagnostic plots |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
468 * a tabular with the differentially expressed genes in categories (GO/KEGG terms) |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
469 * an RData file |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
470 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
471 ----- |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
472 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
473 **Method options** |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
474 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
475 3 methods, *Wallenius*, *Sampling* and *Hypergeometric*, can be used to calculate the p-values as follows. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
476 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
477 *Wallenius* |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
478 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
479 approximates the true distribution of numbers of members of a category amongst DE genes by the Wallenius non-central hypergeometric distribution. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
480 This distribution assumes that within a category all genes have the same probability of being chosen. Therefore, this approximation works best when the range in probabilities obtained by the probability weighting function is small. This is the method used by default. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
481 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
482 *Sampling* |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
483 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
484 uses random sampling to approximate the true distribution and uses it to calculate the p-values for over (and under) representation of categories. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
485 Although this is the most accurate method given a high enough value of sampling number, its use quickly becomes computationally prohibitive. It may sometimes be desirable to use random sampling to generate the null distribution for category |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
486 membership. For example, to check consistency against results from the Wallenius approximation. This is easily accomplished by using the method option to additionally specify sampling and the number of samples to generate. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
487 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
488 *Hypergeometric* |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
489 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
490 assumes there is no bias in power to detect differential expression at all and calculates the p-values using a standard hypergeometric distribution (no length bias correction is performed). Useful if you wish to test the effect of length bias on your results. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
491 Caution: Hypergeometric should NEVER be used for producing results for biological interpretation of RNA-seq data. If length bias is truly not present in your data, goseq will produce a nearly flat PWF plot, no length bias correction will be applied to your data, and all methods will produce the same results. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
492 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
493 ----- |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
494 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
495 **More Information** |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
496 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
497 In order to account for the length bias inherent to RNA-seq data when performing a GO analysis |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
498 (or other category based tests), one cannot simply use the hypergeometric distribution as the null |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
499 distribution for category membership, which is appropriate for data without DE length bias, such |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
500 as microarray data. GO analysis of RNA-seq data requires the use of random sampling in order |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
501 to generate a suitable null distribution for GO category membership and calculate each categories |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
502 significance for over representation amongst DE genes. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
503 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
504 However, this random sampling is computationally expensive. In most cases, the Wallenius |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
505 distribution can be used to approximate the true null distribution, without any significant loss in |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
506 accuracy. The goseq package implements this approximation as its default option. The option |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
507 to generate the null distribution using random sampling is also included as an option, but users |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
508 should be aware that the default number of samples generated will not be enough to accurately |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
509 call enrichment when there are a large number of go terms. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
510 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
511 Having established a null distribution, each category is then tested for over and under |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
512 representation amongst the set of differentially expressed genes and the null is used to calculate a |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
513 p-value for under and over representation. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
514 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
515 Having performed a GO analysis, you may now wish to interpret the results. If you wish to |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
516 identify categories significantly enriched/unenriched below some p-value cutoff, it is necessary to |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
517 first apply some kind of multiple hypothesis testing correction. For example, you can identify GO categories over |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
518 enriched using a 0.05 FDR (p.adjust) cutoff [Benjamini and Hochberg, 1995]. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
519 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
520 Unless you are a machine, GO and KEGG category identifiers are probably not very meaningful to you. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
521 Information about each identifier can be obtained from the `Gene Ontology`_ and KEGG_ websites. |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
522 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
523 .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
524 .. _Gene Ontology: http://www.geneontology.org |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
525 .. _KEGG: http://www.genome.jp/kegg |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
526 |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
527 ]]></help> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
528 <citations> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
529 <citation type="doi">10.1186/gb-2010-11-2-r14</citation> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
530 </citations> |
|
11385d227014
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff
changeset
|
531 </tool> |