# HG changeset patch # User crs4 # Date 1474028698 14400 # Node ID c3f0da6c9ea1af29183c708ef0a9bc2e7fd9b2d1 planemo upload diff -r 000000000000 -r c3f0da6c9ea1 biosample.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biosample.xml Fri Sep 16 08:24:58 2016 -0400 @@ -0,0 +1,247 @@ + + 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 000000000000 -r c3f0da6c9ea1 importer.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/importer.py Fri Sep 16 08:24:58 2016 -0400 @@ -0,0 +1,7 @@ +# BEGIN_COPYRIGHT +# END_COPYRIGHT + +import sys +from bl.vl.app.importer.main import main + +main(sys.argv[1:])