# HG changeset patch # User ric # Date 1474550883 14400 # Node ID f833f23d38a38bec34bba2d563b317034979556d # Parent 43be74e62bfeefc12ab28d228ee0b4bbfea3c695 Deleted selected files diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/biosample.xml --- a/galaxy-tools/biobank/importer/biosample.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,247 +0,0 @@ - - import BioSample definitions within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=${input} - --ofile=${output} - --report_file=${report} - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - biosample - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($source_type) != 'use_provided' - --source-type ${source_type} - #end if - #if str($vessel_type_selector.vessel_type) != 'use_provided' - --vessel-type ${vessel_type_selector.vessel_type} - #end if - #if str($vessel_content) != 'use_provided' - --vessel-content=${vessel_content} - #end if - #if str($vessel_status) != 'use_provided' - --vessel-status=${vessel_status} - #end if - #if str($vessel_type_selector) == 'IlluminaBeadChipArray' - #if str($vessel_type_selector.assay_type) != 'use_provided' - --bead-chip-assay-type=${vessel_type_selector.assay_type} - #end if - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -A biosample record will have, at least, the following fields:: - - label source - I001-bs-2 V932814892 - I002-bs-2 V932814892 - I003-bs-2 None - -Where label is the label of the biosample container. If a 'None' value -has been passed in the source column, the biosample will be imported -as a new unlinked object into the biobanks. Another example, this time -involving DNA samples:: - - label source used_volume current_volume activation_date - I001-dna V932814899 0.3 0.2 17/03/2007 - I002-dna V932814900 0.22 0.2 21/01/2004 - -A special case is when records refer to biosamples contained in plate -wells. In this case, an additional column must be present with the VID -of the corresponding TiterPlate object. For instance:: - - plate label source - V39030 A01 V932814892 - V39031 A02 V932814893 - V39032 A03 V932814894 - -where the label column is now the label of the well position. - -If row and column (optional) are provided, the program will use them; -if they are not provided, it will infer them from label (e.g., J01 -> -row=10, column=1). Missing labels will be generated as:: - - '%s%03d' % (chr(row+ord('A')-1), column) - -A badly formed label will result in the rejection of the record; the -same will happen if label, row and column are inconsistent. The well -will be filled by current_volume material produced by removing -used_volume material taken from the bio material contained in the -vessel identified by source. row and column are base 1. - -If the sample is a IlluminaBeadChipArray the plate column used in the -PlateWell case will become a illumina_array column and a new column, named -bead_chip_assay_type, is required:: - - illumina_array label source bead_chip_assay_type - V1351235 R01C01 V412441 HUMANEXOME_12V1_B - V1351235 R01C02 V351151 HUMANEXOME_12V1_B - V1351235 R02C01 V345115 HUMANEXOME_12V1_B - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/birth_data.xml --- a/galaxy-tools/biobank/importer/birth_data.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ - - import diagnosis data within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - birth_data - #if str($study) != 'use_provided' - --study ${study} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read in a tsv file with the following columns:: - - study individual timestamp birth_date birth_place - ASTUDY V1234 1310057541608 12/03/1978 006171 - ASTUDY V14112 1310057541608 25/04/1983 006149 - ASTUDY V1241 1310057541608 12/03/2001 006172 - ..... - -where birth_place is a valid ISTAT code for an Italian city or a -foreign Country and birth_date must have the dd/mm/YYYY format. - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/data_collection.xml --- a/galaxy-tools/biobank/importer/data_collection.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,125 +0,0 @@ - - import DataCollection definitions within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - data_collection - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($data_sample_type) != 'use_provided' - --data_sample-type=${data_sample_type} - #end if - #if str($label) - --label=${label} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read in a tsv file with the following columns:: - - study label data_sample - BSTUDY dc-01 V0390290 - BSTUDY dc-01 V0390291 - BSTUDY dc-02 V0390292 - BSTUDY dc-02 V390293 - ... - -This will create new DataCollection(s), whose label is defined by the -label column, and link to it, using DataCollectionItem objects, -the DataSample object(s) identified by data_sample (a VID). - -Records that point to an unknown DataSample will abort the data -collection loading. Previously seen collections will be noisily -ignored. It is not legal to use the importer to add items to a -previously known collection. - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/data_object.xml --- a/galaxy-tools/biobank/importer/data_object.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,111 +0,0 @@ - - import DataObject definitions within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - data_object - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($mimetype) != 'use_provided' - --mimetype=${mimetype} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read in a tsv file with the following columns:: - - study path data_sample mimetype size sha1 - - TEST01 file:/share/fs/v039303.cel V2902 x-vl/affymetrix-cel 39090 E909090 - .... - -Records that point to an unknown data sample will be noisily -ignored. The same will happen to records that have the same path of a -previously seen data_object - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/data_sample.xml --- a/galaxy-tools/biobank/importer/data_sample.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,166 +0,0 @@ - - import DataSample definitions within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - data_sample - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($source_type) != 'use_provided' - --source-type=${source_type} - #end if - #if str($device_type) != 'use_provided' - --device-type=${device_type} - #end if - #if str($scanner) != 'use_provided' - --scanner=${scanner} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read in a tsv file with the following columns:: - - study label source device device_type scanner options - ASTUDY foo01 v03909 v9309 Chip v99020 celID=0009099090 - ASTUDY foo02 v03909 v99022 Scanner v99022 conf1=...,conf2=... - .... - -In this example, the first line corresponds to a dataset obtained by -using chip v9309 on scanner v99020, while the second datasample has -been obtained using a technology directly using a scanner, e.g., an -Illumina HiSeq 2000. The '''scanner''' column is there as a -convenience to support a more detailed description of a chip-based -acquisition. - -The general strategy is to decide what data objects should be -instantiated by looking at the chip column and at its corresponding -maker,model,release. - -The optional column '''scanner''', the vid of the scanner device, is -used in cases, such as Affymetrix genotyping, where it is relevant. - -It is also possible to import DataSample(s) that are the results of -processing other DataSample(s). Here is an example:: - - study label source device device_type options - ASTUDY foo01 v03909 v99021 SoftwareProgram conf1=...,conf2=... - ASTUDY foo02 v03909 v99021 SoftwareProgram conf1=...,conf2=... - .... - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/device.xml --- a/galaxy-tools/biobank/importer/device.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,129 +0,0 @@ - - import Device definitions within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - device - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($device_type) != 'use_provided' - --device-type=${device_type} - #end if - #if str($maker) - --maker=${maker} - #end if - #if str($model) - --model=${model} - #end if - #if str($release) - --relese=${release} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read in a tsv file with the following columns:: - - study device_type label barcode maker model release location - BSTUDY Scanner pula01 8989898 Affymetrix GeneChip Scanner 3000 7G Pula bld. 5 - BSTUDY Chip chip001 8329482 Affymetrix Genome-Wide Human SNP Array 6.0 None - -All devices have a type, a label, an optional barcode, a maker, a -model, a release and an optional physical location. In the example -above, in the first line we have defined a scanner, which is -physically located in the building 5 lab in Pula. The second line -defines a chip. - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/diagnosis.xml --- a/galaxy-tools/biobank/importer/diagnosis.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,79 +0,0 @@ - - import diagnosis data within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - diagnosis - #if str($study) != 'use_provided' - --study ${study} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read in a tsv file with the following columns:: - - study individual timestamp diagnosis - ASTUDY V899 1310057541608 icd10-cm:E10 - ASTUDY V899 1310057541608 icd10-cm:G35 - ASTYDY V1806 1310057541608 exclusion-problem_diagnosis - ... - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/enrollment.xml --- a/galaxy-tools/biobank/importer/enrollment.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,108 +0,0 @@ - - Create new enrollmnents for existing individuals within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__) == 1 #importer.py - #else #unauthorized_access.py - #end if - #if str($advanced_configuration.configuration_level) == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - enrollment - #if str($study_label) != 'use_provided' - --study=$study_label - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Import of new enrollments related to existing individuals. -An enrollment is characterized by the following fields:: - - source study label - V044DE795E7F9F42FEB9855288CF577A77 xxx id1 - V06C59B915C0FD47DABE6AE02C731780AF xxx id2 - V01654DCFC5BB640C0BB7EE088194E629D xxx id3 - -where source must be the VID of an existing Individual object, study a -label of an existing Study object and label the enrollment code for -the patient in the study. - -The enrollment sub-operation will retrieve the source individual from -the DB, create a new enrollment related to it and output the VIDs of -newly created enrollments. It is not possible to create two -enrollments with the same code related to the same study, nor is it -possible to enroll a patient twice in the same study, even with -different codes. - - - - - - - \ No newline at end of file diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/illumina_bead_chip_measures.xml --- a/galaxy-tools/biobank/importer/illumina_bead_chip_measures.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,127 +0,0 @@ - - import IlluminaBeadChipMeasures definitions within OMERO - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=${input} - --ofile=${output} - --report_file=${report} - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - illumina_bead_chip_measures - #if str($study) != 'use_provided' - --study=${study} - #end if - #if str($source_type) != 'use_provided' - --source_type=${source_type} - #end if - #if str($action_category) != 'use_provided' - --action_category=${action_category} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read a tsv file with the following columns:: - - study label red_channel green_channel source source_type - ASTUDY CHIP_01_R01C01 V1415151235513 V135135661356161 V351351351551 IlluminaBeadChipArray - ASTUDY CHIP_01_R01C02 V2346262462462 V112395151351623 V135113513223 IlluminaBeadChipArray - ASTUDY CHIP_01_R02C01 V1351362899135 V913977551235981 V100941215192 IlluminaBeadChipArray - -This will create new IlluminaBeadChipMeasures whose labels are defined in the -label column. - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/individual.xml --- a/galaxy-tools/biobank/importer/individual.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,99 +0,0 @@ - - import individual definitions within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=$logfile - #if $blocking_validation - --blocking-validator - #end if - individual - #if str($study) != 'use_provided' - --study $study - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will import a stream of new individual definitions defined by the -following columns:: - - label gender father mother - id2 male id4 id5 - id3 female None None - .... - -It is not possible to import the same individual twice: the related -file rows will be noisily ignored. - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/laneslot.xml --- a/galaxy-tools/biobank/importer/laneslot.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,127 +0,0 @@ - - import LaneSlot definitions within omero.biobank - - importer.py - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=${in_file} - --ofile=${out_file} - --report_file=${report_file} - --loglevel=$__app__.config.vl_loglevel - --logfile=${log_file} - #if $blocking_validation - --blocking-validator - #end if - laneslot - #if str($study) != 'use_provided' - --study=${study} - #end if - #if str($source_type) != 'use_provided' - --source_type=${source_type} - #end if - #if str($content) != 'use_provided' - --content=${content} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -A lane slot record will have the following fields:: - - lane tag content source - V123411 ATCACG DNA V4512415 - V123411 CGATGT DNA V1415512 - V412511 DNA V1909012 - V661251 TGACCA DNA V1123111 - V661251 CTTGTA DNA V1211141 - .... - -the content column can be option if passed as script's input value, -tag column is optional too. - - - - - - - \ No newline at end of file diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/marker_alignment.xml --- a/galaxy-tools/biobank/importer/marker_alignment.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,140 +0,0 @@ - - import marker aligments within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - marker_alignment - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($ref_genome) - --ref-genome ${reg_genome} - #end if - #if str($message) - --message ${message} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read in a tsv file with the following columns:: - - marker_vid ref_genome chromosome pos strand allele copies - V0909090 hg18 10 82938938 True A 1 - V0909091 hg18 1 82938999 True A 2 - V0909092 hg18 1 82938938 True B 2 - ... - -Since pos is relative to 5', if the marker has been aligned on the -other strand, it is the responsibility of the aligner app to report -the actual distance from 5', while, at the same time, registering that -the SNP has actually been aligned on the other strand. - -The chromosome field is an integer field with values in the [1, 26] -range, with 23-26 representing, respectively, the X chromosome, the Y -chromosome, the pseudoautosomal regions (XY) and the mitochondrial DNA -(MT). - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/marker_definition.xml --- a/galaxy-tools/biobank/importer/marker_definition.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,119 +0,0 @@ - - import Marker definitions within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input1 - --ofile=$output1 - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - marker_definition - #if str($study) != 'use_provided' - --study ${study} - #end if - --source ${source} - --context ${context} - --release ${release} - --ref-genome ${ref_genome} - --dbsnp-build ${dbsnp_build} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read in a tsv file with the following columns:: - - label rs_label mask strand allele_a allele_b - SNP_A-1780419 rs6576700 [A/G] TOP A G - ... - -Where label is supposed to be the unique label for this marker in the -(source, context, release) context, rs_label is the dbSNP db label for -this snp (it could be the string ``None`` if not defined or not -known). The column mask contains the SNP definition. The strand column -could either be the actual 'illumina style' strand used to define the -alleles in the alleles columns, or the string 'None', which means that -the alleles in the allele column are defined wrt the mask in the -mask column. - -It will, for each row, convert the mask to the TOP strand following -Illumina conventions and then save a record for it in VL. The saved -tuple is (source, context, release, label, rs_label, TOP_mask). There -are no collision controls. - -It will output a a tsv file with the following columns:: - - study label type vid - ASTUDY SNP_A-xxx Marker V000002222 - ... - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/markers_set.xml --- a/galaxy-tools/biobank/importer/markers_set.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,102 +0,0 @@ - - import Marker definitions within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - markers_set - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($label) - --label ${label} - #end if - #if str($maker) != 'use_provided' - --maker ${maker} - #end if - #if str($model) != 'use_provided' - --model ${model} - #end if - #if str($release) - --release ${release} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read in a tsv file with the following columns:: - - marker_vid marker_indx allele_flip - V902909090 0 False - V902909091 1 False - V902909092 2 True - ... - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/samples_container.xml --- a/galaxy-tools/biobank/importer/samples_container.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,287 +0,0 @@ - - import samples container definitions within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - samples_container - #if str($study) != 'use_provided' - --study=${study} - #end if - #if str($container_type_selector.container_type) != 'use_provided' - --container-type=${container_type_selector.container_type} - #if str($container_type_selector.container_type) == 'TiterPlate' - #if str($container_type_selector.plate_shape) != 'use_provided' - --plate-shape=${container_type_selector.plate_shape} - #end if - #elif str($container_type_selector.container_type) == 'FlowCell' - #if str($container_type_selector.flow_cell_slots) != 'use_provided' - --number-of-slots=${container_type_selector.flow_cell_slots} - #end if - #elif str($container_type_selector.container_type) == 'IlluminaArrayOfArrays' - #if str($container_type_selector.ill_shape) != 'use_provided' - --plate-shape=${container_type_selector.ill_shape} - #end if - #if str($container_type_selector.ill_slots) != 'use_provided' - --number_of_slots=${container_type_selector.ill_slots} - #end if - #if str($container_type_selector.array_type) != 'use_provided' - --illumina-array-type=${container_type_selector.array_type} - #end if - #if str($container_type_selector.array_class) != 'use_provided' - --illumina-array-class=${container_type_selector.array_class} - #end if - #if str($container_type_selector.assay_type) != 'use_provided' - --illumina-assay-type=${container_type_selector.assay_type} - #end if - #end if - #end if - #if str($container_status) != 'use_provided' - --container-status=${container_status} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -A container record will have the following fields:: - - label container_status creation_date - A_CONTAINER USABLE 13/02/2012 - B_CONTAINER INSTOCK 12/01/2001 - C_CONTAINER USABLE 25/04/2012 - .... - -the creation_date column is optional, if not specified current date -will be set as the object's creation date, also the container_status -column can be optional if this values is passed as input parameter. - - -When importing new containers, special fields can be included in the -CSV file depending on the type of the objects that you want to -import. - -For TITER PLATES objects the syntax can be the following:: - - label barcode container_status rows columns - A_TITERPLATE XXYYZZ111 INSTOCK 8 12 - B_TITERPLATE XXYYZZ112 INSTOCK 8 12 - C_TITERPLATE XXYYZZ113 READY 8 12 - .... - -rows and columns values can be optional if these values are passed as -input parameters, barcode column is optional. - -For ILLUMINA ARRAY OF ARRAYS objects the syntax can be the following:: - - label barcode container_status rows columns illumina_array_type illumina_array_class illumina_assay_type - A_ILLARRAY XXYYZZ111 INSTOCK 4 2 BeadChip_12x1Q Slide Infinium_HD - B_ILLARRAY XXYYZZ112 INSTOCK 4 2 BeadChip_12x1Q Slide Infinium_HD - C_ILLARRAY XXYYZZ113 INSTOCK 4 2 BeadChip_12x1Q Slide Infinium_HD - -rows, columns, illumina_array_type, illumina_array_class and illumina_assay_type -can be optional if these values are passed as input parameters, barcode column -is optional. - -For FLOW CELL objects the syntax can be the following:: - - label barcode container_status number_of_slots - A_FLOWCELL XXYYZZ221 INSTOCK 8 - B_FLOWCELL XXYYZZ222 INSTOCK 8 - C_FLOWCELL XXYYZZ223 INSTOCK 8 - .... - -number_of_slots column can be optional if this value is passed as -input paramter, barcode column is optional. - -For LANE objects the syntax can be the following:: - - flow_cell slot container_status - V112441441 1 INSTOCK - V112441441 2 INSTOCK - V112441441 3 INSTOCK - V351145519 1 INSTOCK - V351145519 2 INSTOCK - .... - -for Lane objects, no label column has to be provided, the importer -will automatically calculate the labels for each imported object. - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/sequencing_data_sample.xml --- a/galaxy-tools/biobank/importer/sequencing_data_sample.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,198 +0,0 @@ - - - Import sequencing related DataSample definitions within omero/vl - - - importer.py - --operator=galaxy - --ifile=${input} - --ofile=${output} - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - seq_data_sample - #if str($study) != 'use_provided' - --study=${study} - #end if - #if str($source_type) != 'use_provided' - --source-type=${source_type} - #end if - #if str($seq_dsample_type) != 'use_provided' - --seq-dsample-type=${seq_dsample_type} - #end if - #if str($dsample_status) != 'use_provided' - --status=${dsample_status} - #end if - #if str($device) != 'use_provided' - --device=${device} - #end if - #if str($history) != 'None' - --history=${history} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Will read a tsv file with the following columns:: - - study label source source_type seq_dsample_type status device - FOOBAR seq_out_1 V012141 FlowCell SequencerOutput USABLE V123141 - FOOBAR seq_out_2 V012141 FlowCell SequencerOutput USABLE V123141 - FOOBAR seq_out_3 V1AD124 FlowCell SequencerOutput USABLE V123141 - ... - -where - * seq_dsample_type can assume one of the following values: SequencerOutput, RawSeqDataSample, SeqDataSample - * source_type can assume one of the following values: FlowCell, SequencerOutput, RawSeqDataSample - -study, source_type, seq_dsample_type, status and device columns can be -overwritten by using command line options. - -A special case of the previous file is when seq_dsample_type is -SeqDataSample, in this case a mandatory sample column is required, -this column has to contain IDs of Tube objects. -The file will look like this - - study label source source_type seq_dsample_type status device sample - FOOBAR seq_dsample_1 V041241 SequencerOutput SeqDataSample USABLE VBB2351 V124AA41 - FOOBAR seq_dsample_2 V051561 SequencerOutput SeqDataSample USABLE VBB2351 V4151AAE - FOOBAR seq_dsample_3 V151561 SequencerOutput SeqDataSample USABLE VBB2351 V15199CD - ... - -A file containing ax export of the Galaxy history that produced the -data that are going to be imported can be passed as input parameter, -history details must represented as a string serialized in JSON -format. - - - - - - - diff -r 43be74e62bfe -r f833f23d38a3 galaxy-tools/biobank/importer/vessels_collection.xml --- a/galaxy-tools/biobank/importer/vessels_collection.xml Thu Sep 22 08:57:04 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,111 +0,0 @@ - - import VesselsCollection definitions within omero/vl - - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - vessels_collection - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($vessel_type) != 'use_provided' - --vessel_type=${vessel_type} - #end if - #if str($label) - --label=${label} - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -TODO: add doc here... - - - - - - - -