diff gprofiler_snpense.xml @ 0:f83a08dff6f0 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gprofiler_snpense.xml	Thu Nov 14 06:01:29 2019 -0500
@@ -0,0 +1,77 @@
+<?xml version="1.0"?>
+<tool id="gprofiler_snpense" name="gProfiler SNPense" version="@VERSION@">
+    <description>maps SNP rs-codes to gene names, chromosomal coordinates and variant effects</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
+
+query <- scan('${input.file_name}', character(), quote = "")
+
+response <- gsnpense( query
+                    , filter_na  = ${filter_na}
+                    )
+
+output <- response
+output[['ensgs']] <- vapply(output[['ensgs']], paste, collapse = ",", character(1L))
+output[['gene_names']] <- vapply(output[['gene_names']], paste, collapse = ",", character(1L))
+
+output.colnames = append(colnames(output)[1:(length(colnames(output))-1)], colnames(output[['variants']]))
+write.table(output, file='${output}', quote=FALSE, sep='\t', row.names = FALSE, col.names = output.colnames)
+
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="input" type="data" format="txt" label="Input is whitespace-separated list of SNP IDs to be translated (should start with prefix ’rs’)." />
+        <expand macro="filter_na" />
+        <expand macro="tool_settings"></expand>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="txt" value="example_snpense_query.txt" />
+            <param name="base_url" value="http://biit.cs.ut.ee/gprofiler_archive3/e94_eg41_p11" />
+            <output name="output" ftype="tabular" file="example_snpense_results.txt" sort="true" />
+        </test>
+        <test>
+            <param name="input" ftype="txt" value="example_snpense_query.txt" />
+            <param name="base_url" value="http://biit.cs.ut.ee/gprofiler_archive3/e94_eg41_p11" />
+            <param name="filter_na" value="T" />
+            <output name="output" ftype="tabular" file="example_snpense_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:SNPense tool through its API.
+    g:Profiler g:SNPense maps SNP rs identifiers to chromosome positions, genes and variant effects. Available only
+    for human SNPs.
+
+-----
+
+@REFERENCES@
+
+    ]]></help>
+    <expand macro="citations"></expand>
+</tool>
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