# HG changeset patch
# User iuc
# Date 1676664207 0
# Node ID a2b0feda69333d7a131795deac6984c18b1e0c2e
# Parent 980d2a2e11809f65fc6f19ea3df18531e1670344
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
diff -r 980d2a2e1180 -r a2b0feda6933 macros.xml
--- a/macros.xml Tue Nov 01 16:56:55 2022 +0000
+++ b/macros.xml Fri Feb 17 20:03:27 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
+ ]]>
+
-
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+ outWig['outWigType'] != "None" and outWig['outWigStrand']
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diff -r 980d2a2e1180 -r a2b0feda6933 rg_rnaStar.xml
--- a/rg_rnaStar.xml Tue Nov 01 16:56:55 2022 +0000
+++ b/rg_rnaStar.xml Fri Feb 17 20:03:27 2023 +0000
@@ -1,4 +1,4 @@
-
+
Gapped-read mapper for RNA-seq data
macros.xml
@@ -65,9 +65,9 @@
#end if
#end if
- --quantMode ${quantmode_output.quantMode}
- #if 'TranscriptomeSAM' in str($quantmode_output.quantMode):
- --quantTranscriptomeBan ${quantmode_output.quantTranscriptomeBan}
+ --quantMode ${refGenomeSource.GTFconditional.quantmode_output.quantMode}
+ #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):
+ --quantTranscriptomeBan ${refGenomeSource.GTFconditional.quantmode_output.quantTranscriptomeBan}
#end if
## Output format parameters
@@ -206,9 +206,7 @@
#end if
## Limits
- --limitOutSJoneRead $algo.params.limits.limitOutSJoneRead
- --limitOutSJcollapsed $algo.params.limits.limitOutSJcollapsed
- --limitSjdbInsertNsj $algo.params.limits.limitSjdbInsertNsj
+ @LIMITS@
#else:
## Go with STAR's default algorithmic settings,
## but we need to provide a reasonable default
@@ -238,14 +236,19 @@
--chimOutJunctionFormat 1
#end if
#end if
+
+ ##outWig:
+ @OUTWIG@
&&
## recompress BAM output for smaller file size
samtools view -b -o '$mapped_reads' Aligned.sortedByCoord.out.bam
- #if 'TranscriptomeSAM' in str($quantmode_output.quantMode):
+ #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):
## same recompression for optional transcriptome BM
&&
samtools view -b -o '$transcriptome_mapped_reads' Aligned.toTranscriptome.out.bam
#end if
+ ##outWig:
+ @OUTWIGOUTPUTS@
]]>
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label="Pregenerated splice junctions datasets of your samples" />
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label="Read alignment tags to include in the BAM output"
help="Note on using the XS tag: If the XS tag is used, STAR will filter out alignments with undefined strand (i.e., those containing only non-canonical unannotated junctions). Using this tag is recommended if you plan to use the STAR results with STAR-Fusion. In addition, it is required for compatibility
with Cufflinks if your sequences come from an unstranded library preparation.">
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label="Would you like all alignments with the best score labeled
primary?"/> -->
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+used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." />
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- 'TranscriptomeSAM' in quantmode_output['quantMode']
+ 'TranscriptomeSAM' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']
- 'GeneCounts' in quantmode_output['quantMode']
+ 'GeneCounts' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']
+
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