Mercurial > repos > jjohnson > defuse
changeset 22:68494d6aabeb
Update datamanager and defuse.xml config file generation
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Thu, 27 Jun 2013 13:11:50 -0500 |
parents | 1bc79c9d6165 |
children | e8fc5de0578b |
files | data_manager_conf.xml datamanager_create_reference.xml datatypes_conf.xml defuse.xml |
diffstat | 4 files changed, 63 insertions(+), 9 deletions(-) [+] |
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--- a/data_manager_conf.xml Mon Jun 24 08:12:05 2013 -0500 +++ b/data_manager_conf.xml Thu Jun 27 13:11:50 2013 -0500 @@ -8,12 +8,14 @@ <column name="name" /> <column name="path" output_ref="out_file" > <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" --> <move type="directory"> <!-- Moving a file from the extra files path of "out_file" --> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/defuse</target> <!-- Target Location to store the file, directories are created as needed --> + !-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/defuse</target> <!-- Target Location to store the file, directories are created as needed --> </move> <!-- datamanager_create_reference.py should have copied the defuse config file to the working directory. so if we put the ${dbkey}.config path in this column, defuse.xml can set the data_directory to this this directory. --> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/defuse/${dbkey}.config</value_translation> <!-- Store this value in the final Data Table --> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/defuse/${value}.config</value_translation> <!-- Store this value in the final Data Table --> + <value_translation type="function">abspath</value_translation> </column> </output> </data_table>
--- a/datamanager_create_reference.xml Mon Jun 24 08:12:05 2013 -0500 +++ b/datamanager_create_reference.xml Thu Jun 27 13:11:50 2013 -0500 @@ -118,7 +118,7 @@ </conditional> </inputs> <outputs> - <data name="out_file" format="data_manager_json"/> + <data name="out_file" format="data_manager_json" label="${tool.name} : ${genome.ensembl_genome_version}"/> </outputs> <stdio> <exit_code range="1:" level="fatal" description="Error running Create DeFuse Reference" />
--- a/datatypes_conf.xml Mon Jun 24 08:12:05 2013 -0500 +++ b/datatypes_conf.xml Thu Jun 27 13:11:50 2013 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <datatypes> <registration> - <datatype extension="defuse.conf" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="defuse.conf" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="true"/> </registration> </datatypes>
--- a/defuse.xml Mon Jun 24 08:12:05 2013 -0500 +++ b/defuse.xml Thu Jun 27 13:11:50 2013 -0500 @@ -20,7 +20,7 @@ <param name="index" type="select" label="Select a Reference Dataset" help="if your genome of interest is not listed - contact Galaxy team"> <options from_file="defuse_reference.loc"> <column name="name" index="1"/> - <column name="value" index="2"/> + <column name="value" index="3"/> <filter type="sort_by" column="0" /> <validator type="no_options" message="No indexes are available" /> </options> @@ -77,6 +77,9 @@ but they require considerable diskspace, and should be deleted and purged when no longer needed."/> <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/> </inputs> + <stdio> + <exit_code range="1:" level="fatal" description="Error Running Defuse" /> + </stdio> <outputs> <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/> <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" /> @@ -99,12 +102,11 @@ #set $ds = chr(36) #if $refGenomeSource.genomeSource == "history": #set config_file = $refGenomeSource.config.__str__ -#set #else #set config_file = $refGenomeSource.index.value #end if #set pat = '^\s*([^#=][^=]*?)\s*=\s*(.*?)\s*$' -#set fh = open() +#set fh = open($config_file) #set keys = ['dataset_directory','ensembl_organism','ensembl_prefix','ensembl_version','ensembl_genome_version','ucsc_genome_version','ncbi_organism','ncbi_prefix','chromosomes','mt_chromosome','gene_sources','ig_gene_sources','rrna_gene_sources'] #set kv = [] #for $line in $fh: @@ -146,18 +148,68 @@ /project/db/genomes/Hsapiens/hg19/defuse #end try +# Organism IDs +ensembl_organism = #slurp +#try +$ref_dict['ensembl_organism'] +#except +homo_sapiens +#end try + +ensembl_prefix = #slurp +#try +$ref_dict['ensembl_prefix'] +#except +Homo_sapiens +#end try + +ensembl_version = #slurp +#try +$ref_dict['ensembl_version'] +#except +71 +#end try + +ensembl_genome_version = #slurp +#try +$ref_dict['ensembl_genome_version'] +#except +GRCh37 +#end try + +ucsc_genome_version = #slurp +#try +$ref_dict['ucsc_genome_version'] +#except +hg19 +#end try + +ncbi_organism = #slurp +#try +$ref_dict['ncbi_organism'] +#except +Homo_sapiens +#end try + +ncbi_prefix = #slurp +#try +$ref_dict['ncbi_prefix'] +#except +Hs +#end try + # Input genome and gene models gene_models = #slurp #try $ref_dict['gene_models'] #except -\$(dataset_directory)/Homo_sapiens.GRCh37.62.gtf +\$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).gtf #end try genome_fasta = #slurp #try $ref_dict['genome_fasta'] #except -\$(dataset_directory)/Homo_sapiens.GRCh37.62.dna.chromosome.fa +\$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).dna.chromosomes.fa #end try # Repeat table from ucsc genome browser