# HG changeset patch
# User iuc
# Date 1676664058 0
# Node ID a225487bf618f483dee6e9d9b9292c3bfe7ae81a
# Parent c520a52b5174895643caebffffde95581038ae52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
diff -r c520a52b5174 -r a225487bf618 data_manager/macros.xml
--- a/data_manager/macros.xml Fri Sep 10 16:44:59 2021 +0000
+++ b/data_manager/macros.xml Fri Feb 17 20:00:58 2023 +0000
@@ -1,11 +1,12 @@
-
+ the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
- 2.7.8a
+ 2.7.10b
+ 0
+ 21.01
2.7.4a
+ 1
rnastar_index2x_versioned
- star
- samtools
+ star
+ samtools
+ gzip
@@ -35,7 +38,7 @@
-
@@ -55,8 +58,8 @@
10.1093/bioinformatics/bts635
-
-
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@@ -81,11 +84,16 @@
refgenome.fa &&
+ #end if
mkdir -p tempstargenomedir &&
STAR
--runMode genomeGenerate
--genomeDir 'tempstargenomedir'
- --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}'
+ --genomeFastaFiles refgenome.fa
## Handle difference between indices with/without annotations
#if 'GTFconditional' in $refGenomeSource:
## GTFconditional exists only in STAR, but not STARsolo
@@ -109,6 +117,8 @@
--genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
#end if
--runThreadN \${GALAXY_SLOTS:-4}
+ ## in bytes
+ --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
&&
#end if
]]>
@@ -121,17 +131,15 @@
#else:
'${refGenomeSource.GTFconditional.genomeDir.fields.path}'
## Handle difference between indices with/without annotations
- #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
- #if $refGenomeSource.GTFconditional.sjdbGTFfile:
- --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
- --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
- #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
- --sjdbGTFtagExonParentTranscript Parent
- #end if
+ #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf':
+ --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
+ --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
+ #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
+ --sjdbGTFtagExonParentTranscript Parent
#end if
#end if
- #end if
- ]]>
+ #end if
+ ]]>
+
-
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+ outWig['outWigType'] != "None"
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+ outWig['outWigType'] != "None" and outWig['outWigStrand']
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+ outWig['outWigType'] != "None" and outWig['outWigStrand']
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diff -r c520a52b5174 -r a225487bf618 data_manager/rna_star_index_builder.xml
--- a/data_manager/rna_star_index_builder.xml Fri Sep 10 16:44:59 2021 +0000
+++ b/data_manager/rna_star_index_builder.xml Fri Feb 17 20:00:58 2023 +0000
@@ -1,4 +1,4 @@
-
+
builder