annotate gprofiler_random.xml @ 0:39a063071667 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"

<?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>