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

Uploaded

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+++ b/data_manager/data_manager_snpEff_download.xml	Thu Jan 22 09:14:50 2015 -0500
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+<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.0.0" tool_type="manage_data">
+    <description>Download a new database</description>
+    <requirements>
+        <requirement type="package" version="4.0">snpEff</requirement>
+    </requirements>
+    <command interpreter="python">
+        data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config 
+          --genome_version "$genome_version" "$out_file"
+        </command>
+    <inputs>
+        <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
+            <help>https://snpeff-data.galaxyproject.org/databases/</help>
+            <validator type="regex" message="A genome version name is required">\S+</validator>
+        </param>
+    </inputs>
+
+    <outputs>
+           <data name="out_file" format="data_manager_json" label="${tool.name}"/>
+    </outputs>
+    <stdio>
+        <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+        <exit_code range="1:"  level="fatal"   description="Error" />
+    </stdio>
+    <tests>
+        <test>
+            <param name="genome_version" value="GRCh38.76"/>
+            <output name="out_file">
+                <assert_contents>
+                    <!-- Check that a genome was added -->
+                    <has_text text="GRCh38.76" />
+                    <has_text text="snpeffv_regulationdb" />
+                    <has_text text="snpeffv_annotations" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+
+This tool downloads a SnpEff database and populates data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
+
+To see the list of available SnpEff genomes run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeff4_databases 
+
+The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
+
+
+For details about this tool, please go to 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>
+