Mercurial > repos > cschu > featurecounts_data_manager
changeset 2:b3cd759a0064 draft default tip
Uploaded
| author | cschu |
|---|---|
| date | Sun, 26 Jun 2016 17:04:24 -0400 |
| parents | a297bbcd1c01 |
| children | |
| files | data_manager/featurecounts_gxfloader.xml data_manager/make_json.py data_manager_conf.xml gffdm/data_manager/featurecounts_gxfloader.xml gffdm/data_manager/make_json.py gffdm/data_manager_conf.xml gffdm/tool-data/gene_sets.loc.sample gffdm/tool_data_table_conf.xml.sample gffdm/tool_dependencies.xml tool-data/gene_sets.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 12 files changed, 138 insertions(+), 138 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/featurecounts_gxfloader.xml Sun Jun 26 17:04:24 2016 -0400 @@ -0,0 +1,28 @@ +<?xml version="1.0"?> +<tool id="featurecounts_gxfloader" name="featurecounts" tool_type="manage_data" version="1.0.1"> + <description>GFF/GTF loader</description> + <requirements> + <requirement type="package" version="1.4.6.p5">featurecounts</requirement> + <requirement type="set_environment">FCOUNT_SCRIPT_PATH</requirement> + </requirements> + <stdio> + <exit_code description="Error" level="fatal" range="1:" /> + </stdio> + <!-- <version_command>kraken -version | awk '{print $NF}'</version_command> --> + <command> + <![CDATA[ + mkdir featurecount_gxf && cp "$gxf" featurecount_gxf/ && + cd .. && python \$FCOUNT_SCRIPT_PATH/data_manager/make_json.py --dbkey "${dbkey}" --provider "${provider}" --ref "${ref}"--out "${out_file}" + ]]> + </command> + <inputs> + <param label="Name for this GFF/GTF" name="dbkey" type="text" /> + <param label="Provider for this GFF/GTF" name="provider" type="text" /> + <param label="Reference URL for this GFF/GTF" name="ref" type="text" /> + <param format="gff,gtf,tabular" label="Select history item" multiple="True" name="gxf" type="data" /> + </inputs> + <outputs> + <data format="data_manager_json" name="out_file" /> + </outputs> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/make_json.py Sun Jun 26 17:04:24 2016 -0400 @@ -0,0 +1,33 @@ +import json +import argparse +import os +import shutil + + + +parser = argparse.ArgumentParser(description='Create data manager json.') +parser.add_argument('--dbkey', action='store') +parser.add_argument('--provider', action='store') +parser.add_argument('--ref', action='store') +parser.add_argument('--out', action='store') + +args = parser.parse_args() + +def main(args): + data_manager_entry = {} + data_manager_entry['value'] = args.dbkey.lower() + data_manager_entry['name'] = args.dbkey + data_manager_entry['path'] = '.' + data_manager_entry['ref'] = args.ref + data_manager_entry['provider'] = args.provider + data_manager_json = dict(data_tables=dict(gene_sets=data_manager_entry)) + params = json.loads(open(args.out).read()) + target_directory = params['output_data'][0]['extra_files_path'] + os.mkdir(target_directory) + output_path = os.path.join(os.getcwd(), 'featurecount_gxf') + for filename in os.listdir(output_path): + shutil.move(os.path.join(output_path, filename), target_directory) + file(args.output, 'w').write(json.dumps(data_manager_json)) + +if __name__ == '__main__': + main(args)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Sun Jun 26 17:04:24 2016 -0400 @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/featurecounts_gxfloader.xml" id="featurecounts_gxfloader" version="1.0.0"> + <data_table name="gene_sets"> + <output> + <!-- <name/UID> <dbkey> <path> <provider> <URL/reference*> --> + <column name="value" /> + <column name="dbkey" /> + <column name="path" output_ref="out_file"> + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">featurecount_gxf/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/featurecount_gxf/${value}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + <column name="provider" /> + <column name="ref" /> + </output> + </data_table> + </data_manager> +</data_managers>
--- a/gffdm/data_manager/featurecounts_gxfloader.xml Sun Jun 26 16:58:34 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -<?xml version="1.0"?> -<tool id="featurecounts_gxfloader" name="featurecounts" tool_type="manage_data" version="1.0.1"> - <description>GFF/GTF loader</description> - <requirements> - <requirement type="package" version="1.4.6.p5">featurecounts</requirement> - <requirement type="set_environment">FCOUNT_SCRIPT_PATH</requirement> - </requirements> - <stdio> - <exit_code description="Error" level="fatal" range="1:" /> - </stdio> - <!-- <version_command>kraken -version | awk '{print $NF}'</version_command> --> - <command> - <![CDATA[ - mkdir featurecount_gxf && cp "$gxf" featurecount_gxf/ && - cd .. && python \$FCOUNT_SCRIPT_PATH/data_manager/make_json.py --dbkey "${dbkey}" --provider "${provider}" --ref "${ref}"--out "${out_file}" - ]]> - </command> - <inputs> - <param label="Name for this GFF/GTF" name="dbkey" type="text" /> - <param label="Provider for this GFF/GTF" name="provider" type="text" /> - <param label="Reference URL for this GFF/GTF" name="ref" type="text" /> - <param format="gff,gtf,tabular" label="Select history item" multiple="True" name="gxf" type="data" /> - </inputs> - <outputs> - <data format="data_manager_json" name="out_file" /> - </outputs> - -</tool>
--- a/gffdm/data_manager/make_json.py Sun Jun 26 16:58:34 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ -import json -import argparse -import os -import shutil - - - -parser = argparse.ArgumentParser(description='Create data manager json.') -parser.add_argument('--dbkey', action='store') -parser.add_argument('--provider', action='store') -parser.add_argument('--ref', action='store') -parser.add_argument('--out', action='store') - -args = parser.parse_args() - -def main(args): - data_manager_entry = {} - data_manager_entry['value'] = args.dbkey.lower() - data_manager_entry['name'] = args.dbkey - data_manager_entry['path'] = '.' - data_manager_entry['ref'] = args.ref - data_manager_entry['provider'] = args.provider - data_manager_json = dict(data_tables=dict(gene_sets=data_manager_entry)) - params = json.loads(open(args.out).read()) - target_directory = params['output_data'][0]['extra_files_path'] - os.mkdir(target_directory) - output_path = os.path.join(os.getcwd(), 'featurecount_gxf') - for filename in os.listdir(output_path): - shutil.move(os.path.join(output_path, filename), target_directory) - file(args.output, 'w').write(json.dumps(data_manager_json)) - -if __name__ == '__main__': - main(args)
--- a/gffdm/data_manager_conf.xml Sun Jun 26 16:58:34 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -<?xml version="1.0"?> -<data_managers> - <data_manager tool_file="data_manager/featurecounts_gxfloader.xml" id="featurecounts_gxfloader" version="1.0.0"> - <data_table name="gene_sets"> - <output> - <!-- <name/UID> <dbkey> <path> <provider> <URL/reference*> --> - <column name="value" /> - <column name="dbkey" /> - <column name="path" output_ref="out_file"> - <move type="directory" relativize_symlinks="True"> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">featurecount_gxf/${value}</target> - </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/featurecount_gxf/${value}</value_translation> - <value_translation type="function">abspath</value_translation> - </column> - <column name="provider" /> - <column name="ref" /> - </output> - </data_table> - </data_manager> -</data_managers>
--- a/gffdm/tool-data/gene_sets.loc.sample Sun Jun 26 16:58:34 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -# This is a sample file distributed with Galaxy that enables tools -# to use gene/exon annotations in the GFF/GTF format. You will need -# to add all the gene set annotations in this configuration file. -# Because of this file, galaxy tools are able to access gene annotations -# provided as GFF / GTF files by selecting on: -# - Priorty (defined by the order in the file) -# - Provider -# - dbkey (reference genome id) -# -# The gene_sets.loc file syntax is: -# <name/UID> <dbkey> <path> <provider> <URL/reference*> -# *optional -# -# Please ensure maximally one TAB (\t) between two columns! -# --------------------------------------------------------- -# -# In case you have TWO or MORE providers PER dbkey, the one mentioned -# first in the file, should have the "default" priority. -# - - - -# [UCSC - UCSC Genes: knownGene] - -#hg19.UCSC knownGene (mm/'yy) hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ucsc http://genome.ucsc.edu/ -#hg18.UCSC knownGene (mm/'yy) hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ucsc http://genome.ucsc.edu/ - - - -# [RefSeq Genes: RefGene] -# link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/ - - - -# [ Ensembl] -# link: http://www.ensembl.org/info/data/ftp/index.html - -#Homo_sapiens.GRCh37.74 hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ensembl ftp://ftp.ensembl.org/pub/release-74/gtf/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gz -#Homo_sapiens.NCBI36.54 hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ensembl ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz
--- a/gffdm/tool_data_table_conf.xml.sample Sun Jun 26 16:58:34 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -<?xml version="1.0"?> -<tables> - <!-- Locations of Kraken database in the required format --> - <table name="gene_sets" comment_char="#"> - <columns>value, dbkey, path, provider, ref</columns> - <file path="tool-data/gene_sets.loc" /> - </table> -</tables>
--- a/gffdm/tool_dependencies.xml Sun Jun 26 16:58:34 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <set_environment version="1.0"> - <environment_variable action="set_to" name="FCOUNT_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> - <package name="featurecounts" version="1.4.6.p5"> - <repository changeset_revision="6d669e01c31b" name="package_featurecounts_1_4_6_p5" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gene_sets.loc.sample Sun Jun 26 17:04:24 2016 -0400 @@ -0,0 +1,39 @@ +# This is a sample file distributed with Galaxy that enables tools +# to use gene/exon annotations in the GFF/GTF format. You will need +# to add all the gene set annotations in this configuration file. +# Because of this file, galaxy tools are able to access gene annotations +# provided as GFF / GTF files by selecting on: +# - Priorty (defined by the order in the file) +# - Provider +# - dbkey (reference genome id) +# +# The gene_sets.loc file syntax is: +# <name/UID> <dbkey> <path> <provider> <URL/reference*> +# *optional +# +# Please ensure maximally one TAB (\t) between two columns! +# --------------------------------------------------------- +# +# In case you have TWO or MORE providers PER dbkey, the one mentioned +# first in the file, should have the "default" priority. +# + + + +# [UCSC - UCSC Genes: knownGene] + +#hg19.UCSC knownGene (mm/'yy) hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ucsc http://genome.ucsc.edu/ +#hg18.UCSC knownGene (mm/'yy) hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ucsc http://genome.ucsc.edu/ + + + +# [RefSeq Genes: RefGene] +# link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/ + + + +# [ Ensembl] +# link: http://www.ensembl.org/info/data/ftp/index.html + +#Homo_sapiens.GRCh37.74 hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ensembl ftp://ftp.ensembl.org/pub/release-74/gtf/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gz +#Homo_sapiens.NCBI36.54 hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ensembl ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Jun 26 17:04:24 2016 -0400 @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of Kraken database in the required format --> + <table name="gene_sets" comment_char="#"> + <columns>value, dbkey, path, provider, ref</columns> + <file path="tool-data/gene_sets.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Jun 26 17:04:24 2016 -0400 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="1.0"> + <environment_variable action="set_to" name="FCOUNT_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + <package name="featurecounts" version="1.4.6.p5"> + <repository changeset_revision="6d669e01c31b" name="package_featurecounts_1_4_6_p5" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>