diff gprofiler_orth.xml @ 0:89cf0828d89d 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_orth.xml	Thu Nov 14 06:00:14 2019 -0500
@@ -0,0 +1,96 @@
+<?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>
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