diff data_manager/data_manager_snpEff_databases.xml @ 5:3d9dd4b9fb09 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty

--- a/data_manager/data_manager_snpEff_databases.xml	Tue Apr 04 18:14:37 2017 -0400
+++ b/data_manager/data_manager_snpEff_databases.xml	Tue Apr 18 09:40:03 2017 -0400
@@ -1,44 +1,33 @@
-<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.1.0" tool_type="manage_data">
-	<description>Read the list of available snpEff databases</description>
-	<requirements>
-		<requirement type="package" version="4.1">snpEff</requirement>
-	</requirements>
-        <stdio>
-          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
-          <exit_code range="1:"  level="fatal"   description="Error" />
-        </stdio>
-	<command interpreter="python">
-        data_manager_snpEff_databases.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" "$out_file"
-        </command>
-	<inputs>
-	</inputs>
-	<outputs>
-           <data name="out_file" format="data_manager_json"/>
-	</outputs>
-        <tests>
-            <test>
-                <output name="out_file">
-                    <assert_contents>
-                        <!-- Check that a genome was added -->
-                        <has_text text="GRCh38.76" />
-                    </assert_contents>
-                </output>
-            </test>
-        </tests>
-	<help>
+<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.3k" tool_type="manage_data">
+    <description>Read the list of available SnpEff databases</description>
+    <requirements>
+        <requirement type="package" version="4.3k">snpeff</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/data_manager_snpEff_databases.py' '$out_file'
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+    <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><![CDATA[
+This tool updates 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.
 
-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>
-      <citations>
+For information about SnpEff: http://snpeff.sourceforge.net
+    ]]></help>
+    <citations>
         <citation type="doi">10.4161/fly.19695</citation>
-      </citations>
+    </citations>
 </tool>
-