Mercurial > repos > iuc > snpeff

diff snpEff_create_db.xml @ 29:ca2b512e8d7c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
author iuc
date Mon, 21 Oct 2024 13:56:15 +0000
parents 6322be79bd8e
children
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--- a/snpEff_create_db.xml	Sat Sep 28 16:27:56 2024 +0000
+++ b/snpEff_create_db.xml	Mon Oct 21 13:56:15 2024 +0000
@@ -1,11 +1,11 @@
-<tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy6" profile="22.01">
+<tool id="snpEff_build_gb" name="SnpEff build:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
     <description> database from Genbank or GFF record</description>
     <macros>
         <import>snpEff_macros.xml</import>
     </macros>
     <requirements>
         <expand macro="requirement" />
-        <requirement type="package" version="1.79">biopython</requirement>
+        <requirement type="package" version="1.84">biopython</requirement>
     </requirements>
     <expand macro="stdio" />
     <expand macro="version_command" />
@@ -36,7 +36,7 @@
             ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.${input_type.input_type_selector}' &&
         #end if
 
-        snpEff @JAVA_OPTIONS@ build -v
+        snpEff @JAVA_OPTIONS@ build -noCheckCds -noCheckProtein -v
         -configOption '${genome_version}'.genome='${genome_version}'
         -configOption '${genome_version}'.codonTable='${codon_table}'
         #if str($input_type.input_type_selector) == "gb":
@@ -186,7 +186,7 @@
     <help><![CDATA[
 **What it does**
 
-This tool uses `"snpEff build -genbank"` or `"snpEff build -gff3"` commands to create a snpEff database.
+This tool uses `snpEff build` to create a snpEff database.
 
 ------
 
@@ -201,7 +201,7 @@
 
  .. class:: warningmark
 
- SnpEff errors out on highly fragmented genomes containing multiple scaffolds. This is because a single gene may be split between multiple scaffolds causing SnpEff to crash. If this is happening use GFF route described below.
+ SnpEff errors out on highly fragmented genomes containing multiple scaffolds. This is because a single gene may be split between multiple scaffolds causing SnpEff to crash. If this is happening use the GFF route described below.
 
 -------