Mercurial > repos > ric > test1
changeset 2:47bf0086e082 draft
Deleted selected files
| author | ric |
|---|---|
| date | Thu, 22 Sep 2016 05:44:26 -0400 |
| parents | 32cfb524b957 |
| children | 43be74e62bfe |
| files | biosample.xml importer.py |
| diffstat | 2 files changed, 0 insertions(+), 254 deletions(-) [+] |
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--- a/biosample.xml Fri Sep 16 09:16:34 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>