diff data_manager/data_manager_snpEff_databases.xml @ 0:9ac823a8b328 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_snpEff_databases.xml	Thu Jan 22 09:14:50 2015 -0500
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+<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.0.0" tool_type="manage_data">
+	<description>Read the list of available snpEff databases</description>
+	<requirements>
+		<requirement type="package" version="4.0">snpEff</requirement>
+	</requirements>
+	<command interpreter="python">
+        data_manager_snpEff_databases.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar "$out_file"
+        </command>
+	<inputs>
+	</inputs>
+	<outputs>
+           <data name="out_file" format="data_manager_json"/>
+	</outputs>
+        <stdio>
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range="1:"  level="fatal"   description="Error" />
+        </stdio>
+        <tests>
+            <test>
+                <output name="out_file">
+                    <assert_contents>
+                        <!-- Check that a genome was added -->
+                        <has_text text="GRCh38.76" />
+                    </assert_contents>
+                </output>
+            </test>
+        </tests>
+	<help>
+
+This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
+It should only need to be run once for a snpEff version, 
+since it populates the SnpEff Download data manager from the snpEff config file.
+
+For information about snpEff:    http://snpEff.sourceforge.net
+
+Please cite:
+"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
+
+	</help>
+</tool>
+