diff data_manager/data_manager_snpEff_download.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_download.xml	Tue Apr 04 18:14:37 2017 -0400
+++ b/data_manager/data_manager_snpEff_download.xml	Tue Apr 18 09:40:03 2017 -0400
@@ -1,25 +1,21 @@
-<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="4.3k" tool_type="manage_data">
     <description>Download a new database</description>
     <requirements>
-        <requirement type="package" version="4.1">snpEff</requirement>
+        <requirement type="package" version="4.3k">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 detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/data_manager_snpEff_download.py'
+--genome_version '$genome_version'
+'$out_file'
+    ]]></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>
+        <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)" help="https://snpeff-data.galaxyproject.org/databases/">
             <validator type="regex" message="A genome version name is required">\S+</validator>
         </param>
     </inputs>
 
     <outputs>
-           <data name="out_file" format="data_manager_json" label="${tool.name}"/>
+        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
     </outputs>
     <tests>
         <test>
@@ -34,23 +30,16 @@
             </output>
         </test>
     </tests>
-    <help>
-
-This tool downloads a SnpEff database and populates data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
+    <help><![CDATA[
+This tool downloads a SnpEff database and populates the 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>
-      <citations>
+For details about this tool, please go to http://snpeff.sourceforge.net
+    ]]></help>
+    <citations>
         <citation type="doi">10.4161/fly.19695</citation>
-      </citations>
+    </citations>
 </tool>
-