Mercurial > repos > iuc > snpeff

diff snpeff_get_chr_names.xml @ 24:4c790901c495 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
author iuc
date Fri, 25 Jan 2019 12:29:21 -0500
parents ad77eac03bf1
children c6422110bc0b
line wrap: on
line diff
--- a/snpeff_get_chr_names.xml	Wed Sep 12 14:35:47 2018 -0400
+++ b/snpeff_get_chr_names.xml	Fri Jan 25 12:29:21 2019 -0500
@@ -9,7 +9,7 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-      snpEff dump
+      snpEff @JAVA_OPTIONS@ dump
       #if $snpDb.genomeSrc == 'cached':
         -dataDir ${snpDb.genomeVersion.fields.path}
         $snpDb.genomeVersion
@@ -21,6 +21,7 @@
           -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}'
           '${snpDb.snpeff_db.metadata.genome_version}'
       #else
+        -dataDir "\$PWD/temp"
         -download
         '$snpDb.genome_version'
       #end if
@@ -47,14 +48,14 @@
             <when value="history">
                 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                     <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help>
-                    <options options_filter_attribute="metadata.SNPEFF_VERSION" >
+                    <options options_filter_attribute="metadata.snpeff_version" >
                         <filter type="add_value" value="@SNPEFF_VERSION@" />
                     </options>
-                    <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.SNPEFF_VERSION == "@SNPEFF_VERSION@"</validator>
+                    <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
                 </param>
             </when>
             <when value="named">
-                <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
+                <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)">
                     <help>The list of available databases can be obtained with 'SnpEff databases' tool. If the database name is not found, locate a database here and download it in your history.</help>
                     <validator type="regex" message="A genome version name is required">\S+</validator>
                 </param>
@@ -62,10 +63,10 @@
             <when value="custom">
                 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                     <help>This can only be used on databases in your history that were created using the snpEff build tool.</help>
-                    <options options_filter_attribute="metadata.SNPEFF_VERSION" >
+                    <options options_filter_attribute="metadata.snpeff_version" >
                         <filter type="add_value" value="@SNPEFF_VERSION@" />
                     </options>
-                    <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.SNPEFF_VERSION == "@SNPEFF_VERSION@"</validator>
+                    <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
                 </param>
             </when>
         </conditional>