# HG changeset patch
# User ric
# Date 1474547631 14400
# Node ID 015f2dcc2510dbe362c43216896e275642c2dc1f
# Parent d84735cff8eddd019b74bc783720e46ea20b1d45
Uploaded
diff -r d84735cff8ed -r 015f2dcc2510 boh/biosample.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/biosample.xml Thu Sep 22 08:33:51 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
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+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 d84735cff8ed -r 015f2dcc2510 boh/birth_data.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/birth_data.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,82 @@
+
+ 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
+
+
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+
+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 d84735cff8ed -r 015f2dcc2510 boh/data_collection.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/data_collection.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,125 @@
+
+ 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
+
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+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.
+
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diff -r d84735cff8ed -r 015f2dcc2510 boh/data_object.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/data_object.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,111 @@
+
+ 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
+
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+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
+
+
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+
diff -r d84735cff8ed -r 015f2dcc2510 boh/data_sample.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/data_sample.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,166 @@
+
+ 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
+
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+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 d84735cff8ed -r 015f2dcc2510 boh/device.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/device.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,129 @@
+
+ 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
+
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+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.
+
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+
diff -r d84735cff8ed -r 015f2dcc2510 boh/diagnosis.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/diagnosis.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,79 @@
+
+ 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
+
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+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 d84735cff8ed -r 015f2dcc2510 boh/enrollment.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/enrollment.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,108 @@
+
+ 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
+
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+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 d84735cff8ed -r 015f2dcc2510 boh/group.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/group.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,75 @@
+
+ Create a new group 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=$input1
+ --ofile=$output1
+ --loglevel=$__app__.config.vl_loglevel
+ --logfile=${logfile}
+ group
+ #if str($group_label) != ''
+ --group=$group_label
+ #end if
+
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+Will create a new group of individuals from a file with the following columns::
+
+ study label individual
+ foo I0000 V06C59B915C0FD47DABE6AE02C731780AF
+ foo I0001 V0B718B77691B145BFA8901FCCF6B37998
+ ...
+
+where the column study is optional (it can be provided via the
+group_label param). Labels should be unique within the file and the
+individual field should contain VIDs of existing (within omero/vl)
+Individual objects.
+
+
+
+
+
+
+
diff -r d84735cff8ed -r 015f2dcc2510 boh/illumina_bead_chip_measures.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/illumina_bead_chip_measures.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,127 @@
+
+ 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
+
+
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+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 d84735cff8ed -r 015f2dcc2510 boh/importer.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/importer.py Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,7 @@
+# BEGIN_COPYRIGHT
+# END_COPYRIGHT
+
+import sys
+from bl.vl.app.importer.main import main
+
+main(sys.argv[1:])
diff -r d84735cff8ed -r 015f2dcc2510 boh/individual.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/individual.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,99 @@
+
+ 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 d84735cff8ed -r 015f2dcc2510 boh/laneslot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/laneslot.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,127 @@
+
+ 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 d84735cff8ed -r 015f2dcc2510 boh/marker_alignment.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/marker_alignment.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,140 @@
+
+ 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 d84735cff8ed -r 015f2dcc2510 boh/marker_definition.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/marker_definition.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,119 @@
+
+ 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 d84735cff8ed -r 015f2dcc2510 boh/markers_set.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/markers_set.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,102 @@
+
+ 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 d84735cff8ed -r 015f2dcc2510 boh/samples_container.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/samples_container.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,287 @@
+
+ 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 d84735cff8ed -r 015f2dcc2510 boh/sequencing_data_sample.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/sequencing_data_sample.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,198 @@
+
+
+ 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 d84735cff8ed -r 015f2dcc2510 boh/study.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/study.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,83 @@
+
+ import study 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
+ study
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Will import a stream of new study definitions defined by the following
+tab-separated columns. A typical file will look like the following::
+
+ label description
+ BSTUDY A basically empty description of BSTUDY
+ CSTUDY A basically empty description of CSTUDY
+ ....
+
+
+
+
+
+
+
diff -r d84735cff8ed -r 015f2dcc2510 boh/unauthorized_access.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/unauthorized_access.py Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,6 @@
+# BEGIN_COPYRIGHT
+# END_COPYRIGHT
+
+import sys
+
+sys.exit("You are not authorized to use this tool")
diff -r d84735cff8ed -r 015f2dcc2510 boh/vessels_collection.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/boh/vessels_collection.xml Thu Sep 22 08:33:51 2016 -0400
@@ -0,0 +1,111 @@
+
+ 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...
+
+
+
+
+
+
+
+