Mercurial > repos > iuc > gprofiler_random
diff gprofiler_random.xml @ 0:39a063071667 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
author | iuc |
---|---|
date | Thu, 14 Nov 2019 06:01:04 -0500 |
parents | |
children | 7d18814397a7 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gprofiler_random.xml Thu Nov 14 06:01:04 2019 -0500 @@ -0,0 +1,58 @@ +<?xml version="1.0"?> +<tool id="gprofiler_random" name="gProfiler Random" version="@VERSION@"> + <description>generates a gene list</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="version_command" /> + <command detect_errors="aggressive">Rscript $script_file</command> + <configfiles> + <configfile name="script_file"><![CDATA[ + +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +suppressPackageStartupMessages({ + library("gprofiler2") +}) + +set_user_agent(paste(get_user_agent(), "galaxy")) +sessionInfo() + +response <- random_query(organism = '${organism.organism}') + +write.table(response, file='${output}', quote=FALSE, sep='\t', row.names = FALSE, col.names = FALSE) + + ]]></configfile> + </configfiles> + <inputs> + <expand macro="organism" /> + </inputs> + <outputs> + <data name="output" format="tabular" label="${tool.name}" /> + </outputs> + <tests> + <test> + <output name="output"> + <assert_contents> + <has_n_columns n="1" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ + +**What it does** + This tool performs a request to g:Profiler API to fetch a set of pseudorandom gene IDs. Gene IDs selected in a + way that g:GOSt output with high probability will contain a small number of results with low enough p-values to + be considered as significant. + +----- + +@REFERENCES@ + + ]]></help> + <expand macro="citations"></expand> +</tool> \ No newline at end of file