diff expression_add_biomaterial.xml @ 0:11ec43bed5ea draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 869e5fd8535deca8325777efcd31c70a514b582a
author gga
date Mon, 25 Feb 2019 06:26:58 -0500
parents
children 4843796fcbf6
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/expression_add_biomaterial.xml	Mon Feb 25 06:26:58 2019 -0500
@@ -0,0 +1,42 @@
+<?xml version="1.0"?>
+<tool id="expression_add_biomaterial" name="Create a biomaterial" version="@WRAPPER_VERSION@.0">
+ <description>in Tripal</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <code file="tripal.py"/>
+    <command detect_errors="aggressive"><![CDATA[
+tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"
+
+&&
+
+cp '${file_path}' "\${tmp_dir}/biomaterial_input"
+
+&&
+
+@AUTH@
+
+tripaille expression add_biomaterial
+'$organism_id'
+"\${tmp_dir}/biomaterial_input"
+'$file_path.extension'
+
+&&
+
+echo "Data loaded" > $results
+]]></command>
+    <inputs>
+        <!-- arguments -->
+        <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
+        <param name="file_path" label="Biomaterial description sheet" argument="file_path" type="data" format="xml,tsv,csv" help="A file describing the biomaterial" />
+    </inputs>
+    <outputs>
+        <data format="txt" name="results"/>
+    </outputs>
+    <help>
+Add a new biomaterial to the database
+
+@HELP@
+    </help>
+</tool>