diff gprofiler_random.xml @ 0:39a063071667 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_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>
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