Mercurial > repos > ric > test1
changeset 4:f833f23d38a3 draft
Deleted selected files
| author | ric |
|---|---|
| date | Thu, 22 Sep 2016 09:28:03 -0400 |
| parents | 43be74e62bfe |
| children | 1fcf2875d39d |
| files | galaxy-tools/biobank/importer/biosample.xml galaxy-tools/biobank/importer/birth_data.xml galaxy-tools/biobank/importer/data_collection.xml galaxy-tools/biobank/importer/data_object.xml galaxy-tools/biobank/importer/data_sample.xml galaxy-tools/biobank/importer/device.xml galaxy-tools/biobank/importer/diagnosis.xml galaxy-tools/biobank/importer/enrollment.xml galaxy-tools/biobank/importer/illumina_bead_chip_measures.xml galaxy-tools/biobank/importer/individual.xml galaxy-tools/biobank/importer/laneslot.xml galaxy-tools/biobank/importer/marker_alignment.xml galaxy-tools/biobank/importer/marker_definition.xml galaxy-tools/biobank/importer/markers_set.xml galaxy-tools/biobank/importer/samples_container.xml galaxy-tools/biobank/importer/sequencing_data_sample.xml galaxy-tools/biobank/importer/vessels_collection.xml |
| diffstat | 17 files changed, 0 insertions(+), 2357 deletions(-) [+] |
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--- 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 @@ -<tool id="vl_import_biosample" name="VLI.biosample"> - <description>import BioSample definitions within omero/vl</description> - <command interpreter="python"> - #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 - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="source_type" type="select" - label="type of the source object" - help="Choose from the legal types. See below."> - <option value="use_provided" selected="true"> - Use what provided by record</option> - <option value="Tube">Tube</option> - <option value="PlateWell">PlateWell</option> - <option value="Individual">Individual</option> - <option value="NO_SOURCE">No source provided</option> - </param> - - <conditional name="vessel_type_selector"> - <param name="vessel_type" type="select" - label="type of the vessel object" - help="Choose from the legal types. See below."> - <option value="use_provided" selected="true"> - Use what provided by record - </option> - <option value="Tube">Tube</option> - <option value="PlateWell">PlateWell</option> - <option value="IlluminaBeadChipArray">IlluminaBeadChipArray</option> - </param> - <when value="IlluminaBeadChipArray"> - <param name="assay_type" type="select" label="Illumina Bead Chip Array Assay type" - help="Choose from the following assay types"> - <options from_parameter="tool.app.known_illumina_beadchip_assay_type" - transform_lines="[ "%s%s%s" - % (o[1], self.separator, o[1]) - for o in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide assay type" - value="use_provided" index="0"/> - </options> - </param> - </when> - </conditional> - - <param name="vessel_content" type="select" label="Vessel content" - help="Choose from one of the available values. See below."> - <options from_parameter="tool.app.kb.VesselContent.__enums__" - transform_lines="[ "%s%s%s" - % (e.enum_label(), - self.separator, - e.enum_label()) - for e in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide vessel content" - value="use_provided" index="0"/> - </options> - </param> - <param name="vessel_status" type="select" label="Vessel status" - help="Choose from one of the available values. See below."> - <options from_parameter="tool.app.kb.VesselStatus.__enums__" - transform_lines="[ "%s%s%s" - % (e.enum_label(), - self.separator, - e.enum_label()) - for e in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide vessel status" - value="use_provided" index="0"/> - </options> - </param> - - <conditional name="extra_fields"> - <param name="enabled" type="select" - label="Enable extra optional fields"> - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="current_volume" type="float" - value="20" - help="fluid (FIXME UNITS) currently held in the vessel"> - <validator type="in_range" message="Volume must be positive" - min="0" max="inf"/> - </param> - <param name="used_volume" type="float" - value="20" - help="amount of source fluid (FIXME UNITS) used"> - <validator type="in_range" message="Volume must be positive" - min="0" max="inf"/> - </param> - </when> - </conditional> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What? Me_worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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 - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_birth_data" name="VLI.birth_data"> - <description>import diagnosis data within omero/vl</description> - <command interpreter="python"> - #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 ${study} - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ************************************************** --> - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_data_collection" name="VLI.data_collection"> - <description>import DataCollection definitions within omero/vl</description> - <command interpreter="python"> - #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 - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="label" size="20" type="text" value="" - label="collection label"/> - - <param name="data_sample_type" type="select" - label="Type of the source" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided</option> - <option value="DataSample">DataSample</option> - </param> - - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What? Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_data_object" name="VLI.data_object"> - <description>import DataObject definitions within omero/vl</description> - <command interpreter="python"> - #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 - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="mimetype" type="select" - label="mimetype for the data object." - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided</option> - <option value="x-vl/affymetrix-cel">x-vl/affymetrix-cel</option> - </param> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What? Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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 - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_data_sample" name="VLI.data_sample"> - <description>import DataSample definitions within omero/vl</description> - <command interpreter="python"> - #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 - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="source_type" type="select" - label="Type of the source" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="Individual">Individual</option> - <option value="Tube">Tube</option> - <option value="PlateWell">PlateWell</option> - <option value="DataSample">DataSample</option> - <option value="DataCollectionItem">DataCollectionItem</option> - <option value="IlluminaBeadChipArray">IlluminaBeadChipArray</option> - <option value="IlluminaBeadChipMeasures">IlluminaBeadChipMeasures</option> - </param> - - <param name="device_type" type="select" - label="Type of the device" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided</option> - <option value="Device">Device</option> - <option value="Chip">Chip</option> - <option value="SoftwareProgram">SoftwareProgram</option> - </param> - - <param name="scanner" type="select" label="Scanner used" - help="Choose from the possible scanners. See below."> - <options from_parameter="tool.app.known_scanners" - transform_lines="[ "%s%s%s(%s)" - % ( l[0], self.separator, l[1], l[2]) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="1"/> - <filter type="add_value" name="Records provide scanner ids" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What? Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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=... - .... - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_device" name="VLI.device"> - <description>import Device definitions within omero/vl</description> - <command interpreter="python"> - #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 - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="device_type" type="select" - label="type of the device" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided</option> - <option value="Chip">Chip</option> - <option value="Scanner">Scanner</option> - <option value="SoftwareProgram">SoftwareProgram</option> - <option value="GenotypingProgram">GenotypingProgram</option> - </param> - - <param name="maker" size="40" type="text" value="" label="Device maker"/> - <param name="model" size="40" type="text" value="" label="Device model"/> - <param name="release" size="40" type="text" value="" - label="Device release"/> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_diagnosis" name="VLI.diagnosis"> - <description>import diagnosis data within omero/vl</description> - <command interpreter="python"> - #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 ${study} - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ************************************************** --> - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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 - ... - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_enrollment" name="VLI.enrollment"> - <description>Create new enrollmnents for existing individuals within omero/vl</description> - <command interpreter="python"> - #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 - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study_label" type="select" label="Context study" - help="Choose from already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % (l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records will provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool> \ No newline at end of file
--- 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 @@ -<tool id="vl_import_illumina_bead_chip_measures" name="VLI.illumina_bead_chip_measures"> - <description>import IlluminaBeadChipMeasures definitions within OMERO</description> - <command interpreter="python"> - #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 - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="source_type" type="select" - label="Type of the source" - help="Choose from the following source classes. See below."> - <option value="use_provided" selected="true">Use record provided</option> - <option value="IlluminaBeadChipArray">IlluminaBeadChipArray</option> - </param> - - <param name="action_category" type="select" - label="Action category" - help="Choose from the following action categories. See below."> - <options from_parameter="tool.app.known_action_categories" - transform_lines="[ "%s%s%s" - % ( l[1], self.separator, l[1] ) - for l in obj]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide action category" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ********************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="biobank05.crs4.it" - label="OMERO host"/> - <param name="vl_user" size="40" type="text" value="galaxy" - label="OMERO user"/> - <param name="vl_passwd" size="40" type="text" value="What? Me worry?" - label="OMERO password"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_individual" name="VLI.individual"> - <description>import individual definitions within omero/vl</description> - <command interpreter="python"> - #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 $study - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records will provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_laneslot" name="VLI.laneslot"> - <description>import LaneSlot definitions within omero.biobank</description> - <command interpreter="python"> - 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 - </command> - - <inputs> - <param format="tabular" name="in_file" type="data" - label="A tabular dataset with the following columns..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="source_type" type="select" - label="Type of the source object" - help="Choose from the legal types. Seel below."> - <option value="use_provided" selected="true"> - Records provide source type - </option> - <option value="Tube">Tube</option> - <option value="PlateWell">PlateWell</option> - <option value="Individual">Individual</option> - </param> - - <param name="content" type="select" - label="Type of content" - help="Choose from the legal types. See below."> - <option value="use_provided" selected="true"> - Records provide content type - </option> - <option value="DNA">DNA</option> - <option value="RNA">RNA</option> - </param> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What? Me_worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="out_file" label="${tool.name}.mapping"/> - <data format="tabular" name="report_file" label="${tool.name}.report"/> - <data format="txt" name="log_file" label="${tool.name}.logfile"/> - </outputs> - - <help> -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. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool> \ No newline at end of file
--- 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 @@ -<tool id="vl_import_marker_alignment" name="VLI.marker_alignment"> - <description>import marker aligments within omero/vl</description> - <command interpreter="python"> - #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 - </command> - - <inputs> - <!-- use a special format to automatically pick up the ref-gen --> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See help below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <conditional name="genomeSource"> - <param name="refGenomeSource" - type="select" - label="Will you select a reference genome from your history - or use a built-in index?"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select a reference genome"> - <options from_data_table="libbwa_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" - format="fasta" metadata_name="dbkey" - label="Select a reference from history" /> - </when> - </conditional> - <conditional name="paired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param name="input1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" /> - </when> - <when value="paired"> - <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" /> - <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" /> - </when> - </conditional> - - <param name="source" size="40" type="text" value="" - label="source"/> - <param name="context" size="40" type="text" value="" - label="context"/> - <param name="release" size="40" type="text" value="" - label="release"/> - - - <!-- ************************************************** --> - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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). - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_marker_definition" name="VLI.marker_definition"> - <description>import Marker definitions within omero/vl</description> - <command interpreter="python"> - #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 ${dbsnp_build} - </command> - - <inputs> - <param format="tabular" name="input1" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See help below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="source" size="40" type="text" value="" - optional="false" - label="source"/> - <param name="context" size="40" type="text" value="" - optional="false" - label="context"/> - <param name="release" size="40" type="text" value="" - optional="false" - label="release"/> - <param name="ref_genome" size="40" type="text" value="" - optional="false" - label="reference genome"/> - <param name="dbsnp_build" size="40" type="integer" value="0" - optional="false" - label="dbSNP build"/> - - - <!-- ************************************************** --> - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output1" label="${tool.name}.mapping"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -Will read in a tsv file with the following columns:: - - label rs_label mask strand allele_a allele_b - SNP_A-1780419 rs6576700 <lflank/>[A/G]<rflank/> 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 - ... - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_markers_set" name="VLI.markers_set"> - <description>import Marker definitions within omero/vl</description> - <command interpreter="python"> - #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 ${release} - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See help below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="label" size="40" type="text" value="" - label="label"/> - <param name="maker" size="40" type="text" value="" - label="maker"/> - <param name="model" size="40" type="text" value="" - label="model"/> - <param name="release" size="40" type="text" value="" - label="release"/> - - <!-- ************************************************** --> - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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 - ... - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_samples_container" name="VLI.samples_container"> - <description>import samples container definitions within omero/vl</description> - <command interpreter="python"> - #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 - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <conditional name="container_type_selector"> - <param name="container_type" type="select" label="Container type" - help="Choose from the following container types"> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="TiterPlate">TiterPlate</option> - <option value="FlowCell">Flow Cell</option> - <option value="Lane">Lane</option> - <option value="IlluminaArrayOfArrays">IlluminaArrayOfArrays</option> - </param> - <when value="TiterPlate"> - <param name="plate_shape" type="select" label="Titer Plate's shape" - help="Choose from the following shapes"> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="8x12">8 rows x 12 columns</option> - <option value="32x48">32 rows x 48 columns</option> - </param> - </when> - <when value="FlowCell"> - <param name="flow_cell_slots" type="select" label="Flow Cell slots" - help="Choose from the following list"> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="8">8</option> - </param> - </when> - <when value="IlluminaArrayOfArrays"> - <param name="ill_shape" type="select" label="IlluminArrayOfArrays shape" - help="Choose from the following shapes"> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="6x2">6 rows x 2 columns</option> - <option value="2x6">2 rows x 6 columns</option> - </param> - <param name="ill_slots" type="select" label="IlluminaArrayOfArrays slots" - help="Choose from the following list"> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="12">12</option> - </param> - <param name="array_type" type="select" label="Illumina Array of Arrays type" - help="choose from the following list"> - <options from_parameter="tool.app.known_illumina_array_of_arrays_type" - transform_lines="[ "%s%s%s" - % (o[1], self.separator, o[1]) - for o in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide array type" - value="use_provided" index="0"/> - </options> - </param> - <param name="array_class" type="select" label="Illumina Array of Arrays class" - help="choose from the following list"> - <options from_parameter="tool.app.known_illumina_array_of_arrays_class" - transform_lines="[ "%s%s%s" - % (o[1], self.separator, o[1]) - for o in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide array class" - value="use_provided" index="0"/> - </options> - </param> - <param name="assay_type" type="select" label="Illumina Array of Arrays Assay type" - help="choose from the following list"> - <options from_parameter="tool.app.known_illumina_array_of_arrays_assay_type" - transform_lines="[ "%s%s%s" - % (o[1], self.separator, o[1]) - for o in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide array assay type" - value="use_provided" index="0"/> - </options> - </param> - </when> - </conditional> - - <param name="container_status" type="select" label="Container status" - help="Choose from one of the available values. See below."> - <options from_parameter="tool.app.kb.ContainerStatus.__enums__" - transform_lines="[ "%s%s%s" - % (e.enum_label(), - self.separator, - e.enum_label()) - for e in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide plate status" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_seq_data_sample" name="VLI.seq_data_sample"> - <description> - Import sequencing related DataSample definitions within omero/vl - </description> - <command interpreter="python"> - 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 - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="source_type" type="select" - label="Type of the source" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="FlowCell">FlowCell</option> - <option value="SequencerOutput"> - SequencerOutput - </option> - <option value="RawSeqDataSample"> - RawSeqDataSample - </option> - </param> - - <!-- Choose the device after the type selection, SequencerOutput - will required an HardwareDevice, RawSeqDataSample and SeqDataSample - will required a SoftwareDevice. If the "use provided" is selected, - load a generic Device select list --> - <param name="seq_dsample_type" type="select" - label="Type of the DataSample" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="SequencerOutput"> - SequencerOutput - </option> - <option value="RawSeqDataSample"> - RawSeqDataSample - </option> - <option value="SeqDataSample"> - SeqDataSample - </option> - </param> - - <param name="dsample_status" type="select" label="DataSample status" - help="Choose from one of the available values. See below."> - <options from_parameter="tool.app.known_data_sample_status" - transform_lines="[ "%s%s%s" - % (l[1], self.separator, l[1]) - for l in obj ]"> - <column name="value" index="1"/> - <column name="name" index="0"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide status" - value="use_provided" index="0"/> - </options> - </param> - - <param name="device" type="select" label="device" - help="Choose from the already defined devices. See below."> - <options from_parameter="tool.app.known_devices" - transform_lines = "[ "%s%s%s" - % ( l[0], self.separator, l[1]) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="1"/> - <filter type="add_value" name="Records provide device ids" - value="use_provided" index="0"/> - </options> - </param> - - <param format="txt" name="history" type="data" optional="true" - label="Objects history" - help="Galaxy history in JSON format, history will be shared among all objects"/> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What? Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -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. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- 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 @@ -<tool id="vl_import_vessels_collection" name="VLI.vessels_collection"> - <description>import VesselsCollection definitions within omero/vl</description> - <command interpreter="python"> - #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 - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="label" size="20" type="text" value="" - label="collection label"/> - - <param name="vessel_type" type="select" - label="Type of the source" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided</option> - <option value="Vessel">Vessel</option> - <option value="TiterPlate">TiterPlate</option> - </param> - - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What? Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -TODO: add doc here... - </help> - - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>