Merge pull request #6572 from wm75/snpeff-version-fix

SnpEff: distinguish between tool version and internal snpeff version …
galaxyproject · Nov 18, 2024 · 280d524 · 280d524
2 parents 15ce75a + 6254214
commit 280d524
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Showing 6 changed files with 14 additions and 13 deletions.
diff --git a/tool_collections/snpeff/snpEff.xml b/tool_collections/snpeff/snpEff.xml
@@ -1,4 +1,4 @@
-<tool id="snpEff" name="SnpEff eff:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
+<tool id="snpEff" name="SnpEff eff:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description> annotate variants</description>
     <macros>
         <import>snpEff_macros.xml</import>

diff --git a/tool_collections/snpeff/snpEff_create_db.xml b/tool_collections/snpeff/snpEff_create_db.xml
@@ -1,4 +1,4 @@
-<tool id="snpEff_build_gb" name="SnpEff build:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
+<tool id="snpEff_build_gb" name="SnpEff build:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description> database from Genbank or GFF record</description>
     <macros>
         <import>snpEff_macros.xml</import>

diff --git a/tool_collections/snpeff/snpEff_databases.xml b/tool_collections/snpeff/snpEff_databases.xml
@@ -1,4 +1,4 @@
-<tool id="snpEff_databases" name="SnpEff databases:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
+<tool id="snpEff_databases" name="SnpEff databases:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description> list available databases</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -48,7 +48,7 @@
         </param>
     </inputs>
     <outputs>
-        <data name="snpeff_dbs" format="tabular" label="${tool.name} @SNPEFF_VERSION@ available databases" />
+        <data name="snpeff_dbs" format="tabular" label="@SNPEFF_VERSION@ available databases" />
     </outputs>
     <tests>
         <test>

diff --git a/tool_collections/snpeff/snpEff_download.xml b/tool_collections/snpeff/snpEff_download.xml
@@ -1,4 +1,4 @@
-<tool id="snpEff_download" name="SnpEff download:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
+<tool id="snpEff_download" name="SnpEff download:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description> download a pre-built database</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -19,7 +19,7 @@ mv temp/'$genome_version' '$snpeff_db.files_path'
         </param>
     </inputs>
     <outputs>
-        <data name="snpeff_db" format="snpeffdb" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}"/>
+        <data name="snpeff_db" format="snpeffdb" label="@SNPEFF_VERSION@ ${genome_version} database"/>
     </outputs>
     <tests>
         <test>

diff --git a/tool_collections/snpeff/snpEff_macros.xml b/tool_collections/snpeff/snpEff_macros.xml
@@ -1,8 +1,11 @@
 <macros>
-    <xml name="requirement">
-        <requirement type="package" version="5.2">snpeff</requirement>
-        <yield/>
-    </xml>
+  <token name="@TOOL_VERSION@">5.2</token>
+  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@SNPEFF_VERSION@">SnpEff5.2</token>
+  <xml name="requirement">
+      <requirement type="package" version="@TOOL_VERSION@">snpeff</requirement>
+      <yield/>
+  </xml>
   <xml name="stdio">
     <stdio>
         <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
@@ -14,8 +17,6 @@
 snpEff -version
     ]]></version_command>
   </xml>
-  <token name="@WRAPPER_VERSION@">0</token>
-  <token name="@SNPEFF_VERSION@">5.2</token>
   <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
   <xml name="ref_select">
     <conditional name="reference_source">

diff --git a/tool_collections/snpeff/snpeff_get_chr_names.xml b/tool_collections/snpeff/snpeff_get_chr_names.xml
@@ -1,4 +1,4 @@
-<tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
+<tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>list chromosome names/lengths</description>
     <macros>
         <import>snpEff_macros.xml</import>