diff data_manager/featurecounts_gxfloader.xml @ 2:b3cd759a0064 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/featurecounts_gxfloader.xml	Sun Jun 26 17:04:24 2016 -0400
@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<tool id="featurecounts_gxfloader" name="featurecounts" tool_type="manage_data" version="1.0.1">
+    <description>GFF/GTF loader</description>
+    <requirements>
+        <requirement type="package" version="1.4.6.p5">featurecounts</requirement>
+        <requirement type="set_environment">FCOUNT_SCRIPT_PATH</requirement>
+    </requirements>
+    <stdio>
+        <exit_code description="Error" level="fatal" range="1:" />
+    </stdio>
+    <!-- <version_command>kraken -version | awk '{print $NF}'</version_command> -->
+    <command>
+    <![CDATA[
+        mkdir featurecount_gxf && cp "$gxf" featurecount_gxf/ &&
+        cd .. && python \$FCOUNT_SCRIPT_PATH/data_manager/make_json.py --dbkey "${dbkey}" --provider "${provider}" --ref "${ref}"--out "${out_file}"
+    ]]>
+    </command>
+    <inputs>
+        <param label="Name for this GFF/GTF" name="dbkey" type="text" />
+        <param label="Provider for this GFF/GTF" name="provider" type="text" />
+        <param label="Reference URL for this GFF/GTF" name="ref" type="text" />
+        <param format="gff,gtf,tabular" label="Select history item" multiple="True" name="gxf" type="data" />        
+    </inputs>
+    <outputs>
+        <data format="data_manager_json" name="out_file" />
+    </outputs>
+
+</tool>