view gprofiler_orth.xml @ 0:89cf0828d89d draft

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

<?xml version="1.0"?>
<tool id="gprofiler_orth" name="gProfiler Orth" version="@VERSION@">
    <description>translates gene identifiers between organisms</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()

#if $tool_settings.base_url
    set_base_url('${tool_settings.base_url}')
#end if

#if $max
    mthreshold <- $max
#else
    mthreshold = Inf
#end if

query <- scan('${input.file_name}', character(), quote = "")

response <- gorth( query
                 , source_organism   = '${source.organism}'
                 , target_organism     = '${target.organism}'
                 , numeric_ns = '${numeric_ns}'
                 , mthreshold = mthreshold
                 , filter_na  = ${filter_na}
                 )

output <- response
output.colnames = colnames(output)
write.table(output, file='${output}', quote=FALSE, sep='\t', row.names = FALSE, col.names = output.colnames)

        ]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="input" />
        <expand macro="organism" name="source" label="Source organism" />
        <expand macro="organism" name="target" label="Target organism" hsapiens_selected="false" mmusculus_selected="true" />
        <param name="numeric_ns" type="text" value="" optional="true" label="Numeric IDs treated as" help="The prefix for fully numeric IDs. Check the “Resources” section below for the complete list of supported namespaces (including numeric). E.g., ENTREZGENE_ACC, WIKIGENE_ACC." />
        <param name="max" type="integer" value="" optional="true" label="Maximum number of ortholog names per gene to show" help="Shows all by default." />
        <expand macro="filter_na" />
        <expand macro="tool_settings"></expand>
    </inputs>
    <outputs>
        <data label="${tool.name} on ${on_string}" name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="txt" value="example_query.txt" />
            <param name="base_url" value="http://biit.cs.ut.ee/gprofiler_archive3/e94_eg41_p11" />
            <output name="output" ftype="tabular" file="example_orth_results.txt" sort="true" />
        </test>
        <test>
            <param name="input" ftype="txt" value="example_query_2.txt" />
            <param name="base_url" value="http://biit.cs.ut.ee/gprofiler_archive3/e94_eg41_p11" />
            <conditional name="source">
                <param name="organism" value="mmusculus" />
            </conditional>
            <conditional name="target">
                <param name="organism" value="hsapiens" />
            </conditional>
            <param name="numeric_ns" value="WIKIGENE_ACC" />
            <param name="max" value="1" />
            <param name="filter_na" value="T" />
            <output name="output" ftype="tabular" file="example_orth_results_2.txt" sort="true" />
        </test>
    </tests>

    <help><![CDATA[

**What it does**
  This tool wraps gprofiler2 R package which performs a request to g:Profiler g:Orth tool through its API.
    g:Profiler g:Orth retrieves the genes of the target organism that are similar in sequence to the source organism
    genes in the input.

-----

@REFERENCES@

    ]]></help>
    <expand macro="citations"></expand>
</tool>