Mercurial > repos > iuc > data_manager_snpeff

diff data_manager/data_manager_snpEff_databases.xml @ 4:847b0f43c0e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:14:37 -0400
parents e5a471c4630e
children 3d9dd4b9fb09
line wrap: on
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--- a/data_manager/data_manager_snpEff_databases.xml	Mon Oct 31 08:13:11 2016 -0400
+++ b/data_manager/data_manager_snpEff_databases.xml	Tue Apr 04 18:14:37 2017 -0400
@@ -1,23 +1,20 @@
-<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="@WRAPPER_VERSION@.0" tool_type="manage_data">
-    <description>Read the list of available snpEff databases</description>
-    <macros>
-        <import>snpEff_macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-    <command><![CDATA[
-        @CONDA_SNPEFF_JAR_PATH@ &&
-        python '$__tool_directory__/data_manager_snpEff_databases.py' 
-            --jar_path '\$SNPEFF_JAR_PATH/snpEff.jar'
-            '$out_file'
-        ]]>
-    </command>
-    <inputs>
-    </inputs>
-    <outputs>
+<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>
+	</outputs>
         <tests>
             <test>
                 <output name="out_file">
@@ -28,7 +25,7 @@
                 </output>
             </test>
         </tests>
-    <help>
+	<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, 
@@ -39,7 +36,9 @@
 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>
-    <expand macro="citations" />
+	</help>
+      <citations>
+        <citation type="doi">10.4161/fly.19695</citation>
+      </citations>
 </tool>