Mercurial > repos > iuc > data_manager_snpeff

diff data_manager/data_manager_snpEff_download.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_download.xml	Mon Oct 31 08:13:11 2016 -0400
+++ b/data_manager/data_manager_snpEff_download.xml	Tue Apr 04 18:14:37 2017 -0400
@@ -1,17 +1,16 @@
-<tool id="data_manager_snpeff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0" tool_type="manage_data">
+<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.1.0" tool_type="manage_data">
     <description>Download a new database</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 $__tool_directory__/data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
+    <requirements>
+        <requirement type="package" version="4.1">snpEff</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
+        <exit_code range="1:" level="fatal" description="Error" />
+    </stdio>
+    <command interpreter="python">
+        data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
           --genome_version "$genome_version" "$out_file"
-        ]]>
-    </command>
+        </command>
     <inputs>
         <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
             <help>https://snpeff-data.galaxyproject.org/databases/</help>
@@ -50,6 +49,8 @@
 "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" />
+      <citations>
+        <citation type="doi">10.4161/fly.19695</citation>
+      </citations>
 </tool>