Mercurial > repos > iuc > data_manager_snpeff

diff data_manager/data_manager_snpEff_download.xml @ 3:e5a471c4630e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
author iuc
date Mon, 31 Oct 2016 08:13:11 -0400
parents 85a23e2dd92b
children 847b0f43c0e5
line wrap: on
line diff
--- a/data_manager/data_manager_snpEff_download.xml	Tue Jun 07 15:44:15 2016 -0400
+++ b/data_manager/data_manager_snpEff_download.xml	Mon Oct 31 08:13:11 2016 -0400
@@ -1,16 +1,17 @@
-<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.1.0" tool_type="manage_data">
+<tool id="data_manager_snpeff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0" tool_type="manage_data">
     <description>Download a new database</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_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
+    <macros>
+        <import>snpEff_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
+        @CONDA_SNPEFF_JAR_PATH@ &&
+        python $__tool_directory__/data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
           --genome_version "$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>
@@ -49,8 +50,6 @@
 "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>
-        <citation type="doi">10.4161/fly.19695</citation>
-      </citations>
+    <expand macro="citations" />
 </tool>