# 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 - - + + @@ -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 + ]]> + - + @@ -245,4 +258,143 @@ + + + + + + + + + + + +
+ + + +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + outWig['outWigType'] != "None" + + + + + + + outWig['outWigType'] != "None" + + + + + + + outWig['outWigType'] != "None" and outWig['outWigStrand'] + + + + + + + outWig['outWigType'] != "None" and outWig['outWigStrand'] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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