# HG changeset patch
# User iuc
# Date 1492775939 14400
# Node ID 318b2a9d54dd52ca730330371b974c697f6b940a
# Parent ace9f5a2b40f27432107906fc8d1f6a15510cc0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
diff -r ace9f5a2b40f -r 318b2a9d54dd README.rst
--- a/README.rst Fri Feb 05 11:56:20 2016 -0500
+++ b/README.rst Fri Apr 21 07:58:59 2017 -0400
@@ -3,5 +3,7 @@
===================
- **Memory**: To run efficiently, RNA-STAR requires enough free memory to
- hold the SA-indexed reference genome in RAM. For Human Genome hg19 this is
- index about 27GB and running RNA-STAR requires approximately ~30GB of RAM.
+ hold the SA-indexed reference genome in RAM. For Human Genome hg19 this
+ index is about 27GB and running RNA-STAR requires approximately ~30GB of RAM.
+ For custom genomes, the rule of thub is to multiply the size of the
+ reference FASTA file by 9 to estimated required amount of RAM.
diff -r ace9f5a2b40f -r 318b2a9d54dd macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Apr 21 07:58:59 2017 -0400
@@ -0,0 +1,20 @@
+
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+ star
+ samtools
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+ --readFilesCommand zcat
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+ 10.1093/bioinformatics/bts635
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diff -r ace9f5a2b40f -r 318b2a9d54dd rg_rnaStar.xml
--- a/rg_rnaStar.xml Fri Feb 05 11:56:20 2016 -0500
+++ b/rg_rnaStar.xml Fri Apr 21 07:58:59 2017 -0400
@@ -1,143 +1,175 @@
-
+Gapped-read mapper for RNA-seq data
-
- rnastar
- samtools
-
+
+ macros.xml
+
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/dev/null
-
## Convert chimeric reads.
- #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.segmentMin) > 0 ):
- && samtools view -@ \${GALAXY_SLOTS:-4} -Shb Chimeric.out.sam | samtools sort -@ \${GALAXY_SLOTS:-4} - ChimericSorted 2>/dev/null
+ #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0 ):
+ &&
+ samtools view
+ -@ \${GALAXY_SLOTS:-4}
+ -Shb Chimeric.out.sam |
+
+ samtools sort
+ -@ \${GALAXY_SLOTS:-4} - ChimericSorted
#end if
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- params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['segmentMin'] > 0 )
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+ params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )
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- params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['segmentMin'] > 0 )
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+ params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )
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**What it does**
-This tool runs STAR, an ultrafast universal RNA-seq aligner.
+STAR is an ultrafast universal RNA-seq aligner.
**Extra SAM attributes**
@@ -500,10 +563,6 @@
**Attributions**
-Note that each component has its own license:
- - RNA STAR: GPLv3
- - samtools: MIT/Expat License
-
rna_star - see the web site at rna_star_
For details, please see the rna_starMS_
@@ -525,8 +584,6 @@
.. _rna_star: https://github.com/alexdobin/STAR
.. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full
.. _Galaxy: http://getgalaxy.org
-
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- 10.1093/bioinformatics/bts635
-
+
+
diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/rnastar_test.log
--- a/test-data/rnastar_test.log Fri Feb 05 11:56:20 2016 -0500
+++ b/test-data/rnastar_test.log Fri Apr 21 07:58:59 2017 -0400
@@ -1,7 +1,7 @@
- Started job on | Feb 18 14:00:29
- Started mapping on | Feb 18 14:00:32
- Finished on | Feb 18 14:00:33
- Mapping speed, Million of reads per hour | 0.36
+ Started job on | Mar 01 15:54:22
+ Started mapping on | Mar 01 15:54:25
+ Finished on | Mar 01 15:54:25
+ Mapping speed, Million of reads per hour | inf
Number of input reads | 100
Average input read length | 75
@@ -29,3 +29,6 @@
% of reads unmapped: too many mismatches | 0.00%
% of reads unmapped: too short | 0.00%
% of reads unmapped: other | 0.00%
+ CHIMERIC READS:
+ Number of chimeric reads | 0
+ % of chimeric reads | 0.00%
diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/rnastar_test2.log
--- a/test-data/rnastar_test2.log Fri Feb 05 11:56:20 2016 -0500
+++ b/test-data/rnastar_test2.log Fri Apr 21 07:58:59 2017 -0400
@@ -1,7 +1,7 @@
- Started job on | Jul 23 12:00:42
- Started mapping on | Jul 23 12:00:42
- Finished on | Jul 23 12:00:43
- Mapping speed, Million of reads per hour | 0.36
+ Started job on | Mar 01 15:53:05
+ Started mapping on | Mar 01 15:53:08
+ Finished on | Mar 01 15:53:08
+ Mapping speed, Million of reads per hour | inf
Number of input reads | 100
Average input read length | 75
@@ -29,3 +29,6 @@
% of reads unmapped: too many mismatches | 0.00%
% of reads unmapped: too short | 10.00%
% of reads unmapped: other | 0.00%
+ CHIMERIC READS:
+ Number of chimeric reads | 0
+ % of chimeric reads | 0.00%
diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/rnastar_test2_mapped_reads.bam
Binary file test-data/rnastar_test2_mapped_reads.bam has changed
diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/rnastar_test_mapped_reads.bam
Binary file test-data/rnastar_test_mapped_reads.bam has changed
diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/test1.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.gtf Fri Apr 21 07:58:59 2017 -0400
@@ -0,0 +1,4 @@
+test_chromosome test gene 1 650 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1";
+test_chromosome test transcript 1 650 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1";
+test_chromosome test exon 1 650 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1";
+test_chromosome test CDS 100 550 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1";
diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/test3.fastqsanger.gz
Binary file test-data/test3.fastqsanger.gz has changed
diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/tophat_test_reads_per_gene.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat_test_reads_per_gene.txt Fri Apr 21 07:58:59 2017 -0400
@@ -0,0 +1,5 @@
+N_unmapped 0 0 0
+N_multimapping 1 1 1
+N_noFeature 0 51 48
+N_ambiguous 0 0 0
+GENE1 99 48 51
diff -r ace9f5a2b40f -r 318b2a9d54dd tool-data/rnastar_index.loc.sample
--- a/tool-data/rnastar_index.loc.sample Fri Feb 05 11:56:20 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of rna-star indexed sequences data files. You will
-#need to create these data files and then create a bowtie_indices.loc
-#file similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The bowtie2_indices.loc
-#file has this format (longer white space characters are TAB characters):
-#
-#
-#
-#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar
-
diff -r ace9f5a2b40f -r 318b2a9d54dd tool-data/rnastar_index2.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rnastar_index2.loc.sample Fri Apr 21 07:58:59 2017 -0400
@@ -0,0 +1,23 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of rna-star indexed sequences data files. You will
+#need to create these data files and then create a rnastar_index2.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The rnastar_index2.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#The column should be 1 or 0, indicating whether the index was made
+#with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not,
+#respecively.
+#
+#Note that STAR indices can become quite large. Consequently, it is only
+#advisable to create indices with annotations if it's known ahead of time that
+#(A) the annotations won't be frequently updated and (B) the read lengths used
+#will also rarely vary. If either of these is not the case, it's advisable to
+#create indices without annotations and then specify an annotation file and
+#maximum read length (minus 1) when running STAR.
+#
+#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0
+#hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1
+
diff -r ace9f5a2b40f -r 318b2a9d54dd tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Fri Feb 05 11:56:20 2016 -0500
+++ b/tool_data_table_conf.xml.sample Fri Apr 21 07:58:59 2017 -0400
@@ -1,7 +1,7 @@
-
- value, dbkey, name, path
-
+
+ value, dbkey, name, path, with-gtf
+
diff -r ace9f5a2b40f -r 318b2a9d54dd tool_dependencies.xml
--- a/tool_dependencies.xml Fri Feb 05 11:56:20 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-
-
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- Installs the STAR wrapper and dependency packages samtools and star - see https://code.google.com/p/rna-star/
- STAR is a very fast mapper for rna-seq giving junctions if the indexes are constructed with a junction library
-
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