Mercurial > repos > sblanck > smagexp
annotate MetaRNAseq.xml @ 4:58052f8bc987 draft
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 8d4651e98155855108d1c4574392d503cc04bc95
| author | sblanck |
|---|---|
| date | Thu, 01 Mar 2018 05:22:24 -0500 |
| parents | 63355796cdc8 |
| children | 3ce32282f6a4 |
| rev | line source |
|---|---|
|
0
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
1 <tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.0.0"> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
2 |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
3 <description>Performs meta-analysis thanks to metaRNAseq</description> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
4 |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
5 <requirements> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
6 <requirement type="package">bioconductor-affy</requirement> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
7 <requirement type="package">bioconductor-annaffy</requirement> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
8 <requirement type="package">bioconductor-geoquery</requirement> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
9 <requirement type="package">r-venndiagram</requirement> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
10 <requirement type="package">r-jsonlite</requirement> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
11 <requirement type="package">r-metarnaseq</requirement> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
12 <requirement type="package">r-optparse</requirement> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
13 </requirements> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
14 |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
15 <stdio> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
16 <exit_code range="1:" /> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
17 <regex match="Warning" source="both" level="warning"/> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
18 </stdio> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
19 |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
20 <command> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
21 |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
22 <![CDATA[ |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
23 Rscript |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
24 ${__tool_directory__}/MetaRNASeq.R |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
25 --input "#for $input in $inputs# $input;$input.name, #end for#" |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
26 --result $top_table |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
27 --htmloutput $result_html |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
28 --htmloutputpath $result_html.extra_files_path |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
29 --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
30 ]]> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
31 </command> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
32 |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
33 <inputs> |
|
2
f18413a94742
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit b53a3997a880872df62a84370133b9a955e70418
sblanck
parents:
0
diff
changeset
|
34 <param format="tabular" name="inputs" multiple="true" type="data" optional="false" label="Counts file" help="Must have the same number of row in each study. The experimental conditions must be specified in the header of each file"/> |
|
0
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
35 </inputs> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
36 |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
37 <outputs> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
38 <data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/> |
|
3
63355796cdc8
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit ecb5d3451f1623e0cc649ac5197e66995ce19eef
sblanck
parents:
2
diff
changeset
|
39 <data format="html" name="result_html" label="Charts for ${tool.name} on ${on_string}"/> |
|
0
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
40 </outputs> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
41 |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
42 <tests> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
43 |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
44 </tests> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
45 |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
46 <help> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
47 |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
48 </help> |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
49 |
|
1024245abc70
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
sblanck
parents:
diff
changeset
|
50 </tool> |