diff macros.xml @ 28:3e94726bfa9d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
author iuc
date Sun, 11 Feb 2024 00:01:54 +0000
parents 79de45b5069b
children b0f2be869d6d
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line diff
--- a/macros.xml	Fri Sep 01 13:17:29 2023 +0000
+++ b/macros.xml	Sun Feb 11 00:01:54 2024 +0000
@@ -4,8 +4,8 @@
     The data manager uses a symlink to this macro file to keep the STAR and
     the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
     <!-- STAR version to be used -->
-    <token name="@TOOL_VERSION@">2.7.10b</token>
-    <token name="@VERSION_SUFFIX@">4</token>
+    <token name="@TOOL_VERSION@">2.7.11a</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <!-- STAR index version compatible with this version of STAR
     This is the STAR version that introduced the index structure expected
@@ -15,14 +15,14 @@
     or by looking for the versionGenome parameter in source/parametersDefault
     of STAR's source code -->
     <token name="@IDX_VERSION@">2.7.4a</token>
-    <token name="@IDX_VERSION_SUFFIX@">1</token>
+    <token name="@IDX_VERSION_SUFFIX@">0</token>
     <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
 
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">star</requirement>
-            <requirement type="package" version="1.16.1">samtools</requirement>
-            <requirement type="package" version="1.12">gzip</requirement>
+            <requirement type="package" version="1.18">samtools</requirement>
+            <requirement type="package" version="1.13">gzip</requirement>
             <yield />
         </requirements>
     </xml>
@@ -122,6 +122,13 @@
             #if str($refGenomeSource.genomeSAindexNbases):
                 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
             #end if
+            ## Diploid mode
+            #if 'diploidconditional' in $refGenomeSource:
+                #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
+                    --genomeTransformVCF '${refGenomeSource.diploidconditional.genomeTransformVCF}'
+                    --genomeTransformType Diploid
+                #end if   
+            #end if
             --runThreadN \${GALAXY_SLOTS:-4}
             ## in bytes
             --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))