Mercurial > repos > iuc > gprofiler_random

comparison gprofiler_random.xml @ 0:1de9573c661d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
author iuc
date Thu, 14 Nov 2019 10:58:39 +0000
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children 2166cf27c8ef
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-1:000000000000 0:1de9573c661d
1 <?xml version="1.0"?>
2 <tool id="gprofiler_random" name="gProfiler Random" version="@VERSION@">
3 <description>generates a gene list</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"></expand>
8 <expand macro="version_command" />
9 <command detect_errors="aggressive">Rscript $script_file</command>
10 <configfiles>
11 <configfile name="script_file"><![CDATA[
12
13 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
14 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
15
16 suppressPackageStartupMessages({
17 library("gprofiler2")
18 })
19
20 set_user_agent(paste(get_user_agent(), "galaxy"))
21 sessionInfo()
22
23 response <- random_query(organism = '${organism.organism}')
24
25 write.table(response, file='${output}', quote=FALSE, sep='\t', row.names = FALSE, col.names = FALSE)
26
27 ]]></configfile>
28 </configfiles>
29 <inputs>
30 <expand macro="organism" />
31 </inputs>
32 <outputs>
33 <data name="output" format="tabular" label="${tool.name}" />
34 </outputs>
35 <tests>
36 <test>
37 <output name="output">
38 <assert_contents>
39 <has_n_columns n="1" />
40 </assert_contents>
41 </output>
42 </test>
43 </tests>
44
45 <help><![CDATA[
46
47 **What it does**
48 This tool performs a request to g:Profiler API to fetch a set of pseudorandom gene IDs. Gene IDs selected in a
49 way that g:GOSt output with high probability will contain a small number of results with low enough p-values to
50 be considered as significant.
51
52 -----
53
54 @REFERENCES@
55
56 ]]></help>
57 <expand macro="citations"></expand>
58 </tool>