# HG changeset patch
# User iuc
# Date 1565883016 14400
# Node ID f5eb9afa8f8ac30264c9e931a2c05b3998df0927
# Parent 6ef6520f14fce591faaeb0587aedbc8a60d8a839
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
diff -r 6ef6520f14fc -r f5eb9afa8f8a data_manager/macros.xml
--- a/data_manager/macros.xml Wed Jul 18 13:26:12 2018 -0400
+++ b/data_manager/macros.xml Thu Aug 15 11:30:16 2019 -0400
@@ -1,10 +1,39 @@
+
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+ 2.7.2a
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+ 2.7.1a
+
- star
- samtools
+ star
+ samtools
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--readFilesCommand zcat
@@ -13,8 +42,8 @@
10.1093/bioinformatics/bts635
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@@ -22,7 +51,7 @@
-
@@ -36,4 +65,99 @@
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diff -r 6ef6520f14fc -r f5eb9afa8f8a data_manager/rna_star_index_builder.py
--- a/data_manager/rna_star_index_builder.py Wed Jul 18 13:26:12 2018 -0400
+++ b/data_manager/rna_star_index_builder.py Thu Aug 15 11:30:16 2019 -0400
@@ -1,29 +1,31 @@
#!/usr/bin/env python
+import argparse
import json
-import optparse
def main():
- parser = optparse.OptionParser()
- parser.add_option( '--config-file', dest='config_file', action='store', type="string")
- parser.add_option( '--value', dest='value', action='store', type="string" )
- parser.add_option( '--dbkey', dest='dbkey', action='store', type="string" )
- parser.add_option( '--name', dest='name', action='store', type="string" )
- parser.add_option( '--subdir', dest='subdir', action='store', type="string" )
- parser.add_option( '--data-table', dest='data_table', action='store', type="string" )
- parser.add_option( '--withGTF', dest='withGTF', action='store_true' )
- (options, args) = parser.parse_args()
+ parser = argparse.ArgumentParser()
+ parser.add_argument( '--config-file' )
+ parser.add_argument( '--value' )
+ parser.add_argument( '--dbkey' )
+ parser.add_argument( '--name' )
+ parser.add_argument( '--subdir' )
+ parser.add_argument( '--data-table' )
+ parser.add_argument( '--with-gene-model', action='store_true' )
+ parser.add_argument( '--index-version' )
- if options.dbkey in [ None, '', '?' ]:
- raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.dbkey ) )
+ args = parser.parse_args()
+
+ if args.dbkey in [ None, '', '?' ]:
+ raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( args.dbkey ) )
- withGTF = "0"
- if options.withGTF:
- withGTF = "1"
+ with_gene_model = "0"
+ if args.with_gene_model:
+ with_gene_model = "1"
- data_manager_dict = {'data_tables': {options.data_table: [dict({"value": options.value, "dbkey": options.dbkey, "name": options.name, "path": options.subdir, "with-gtf": withGTF} )]}}
- open( options.config_file, 'wb' ).write( json.dumps( data_manager_dict ) )
+ data_manager_dict = {'data_tables': {args.data_table: [dict({"value": args.value, "dbkey": args.dbkey, "name": args.name, "path": args.subdir, "with_gene_model": with_gene_model, "version": args.index_version} )]}}
+ open( args.config_file, 'w' ).write( json.dumps( data_manager_dict ) )
if __name__ == "__main__":
diff -r 6ef6520f14fc -r f5eb9afa8f8a data_manager/rna_star_index_builder.xml
--- a/data_manager/rna_star_index_builder.xml Wed Jul 18 13:26:12 2018 -0400
+++ b/data_manager/rna_star_index_builder.xml Thu Aug 15 11:30:16 2019 -0400
@@ -1,4 +1,4 @@
-
+builder
@@ -41,15 +41,16 @@
--config-file '${out_file}'
--value '${all_fasta_source.fields.value}'
--dbkey '${all_fasta_source.fields.dbkey}'
+--index-version '@IDX_VERSION@'
#if $name:
--name '$name'
#else
--name '${all_fasta_source.fields.name}'
#end if
#if str($GTFconditional.GTFselect) == "withGTF":
- --withGTF 1
+ --with-gene-model
#end if
---data-table rnastar_index2
+--data-table rnastar_index2_versioned
--subdir '${subdir}'
]]>
diff -r 6ef6520f14fc -r f5eb9afa8f8a data_manager_conf.xml
--- a/data_manager_conf.xml Wed Jul 18 13:26:12 2018 -0400
+++ b/data_manager_conf.xml Thu Aug 15 11:30:16 2019 -0400
@@ -1,7 +1,7 @@
-
-
+
+
diff -r 6ef6520f14fc -r f5eb9afa8f8a tool-data/rnastar_index2.loc.sample
--- a/tool-data/rnastar_index2.loc.sample Wed Jul 18 13:26:12 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +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 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 6ef6520f14fc -r f5eb9afa8f8a tool-data/rnastar_index2_versioned.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rnastar_index2_versioned.loc.sample Thu Aug 15 11:30:16 2019 -0400
@@ -0,0 +1,26 @@
+#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 built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used)
+#or not.
+#
+#The column indicates the STAR version that introduced the format of
+#the index, i.e., the oldest STAR version that could make use of the index.
+#
+#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 2.7.1a
+#hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a
+
diff -r 6ef6520f14fc -r f5eb9afa8f8a tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Wed Jul 18 13:26:12 2018 -0400
+++ b/tool_data_table_conf.xml.sample Thu Aug 15 11:30:16 2019 -0400
@@ -4,9 +4,9 @@
value, dbkey, name, path
-
-
- value, dbkey, name, path, with-gtf
-
+
+
+ value, dbkey, name, path, with_gene_model, version
+