Mercurial > repos > ric > test
changeset 11:015f2dcc2510 draft
Uploaded
| author | ric |
|---|---|
| date | Thu, 22 Sep 2016 08:33:51 -0400 |
| parents | d84735cff8ed |
| children | 8fdf5996c0fb |
| files | boh/biosample.xml boh/birth_data.xml boh/data_collection.xml boh/data_object.xml boh/data_sample.xml boh/device.xml boh/diagnosis.xml boh/enrollment.xml boh/group.xml boh/illumina_bead_chip_measures.xml boh/importer.py boh/individual.xml boh/laneslot.xml boh/marker_alignment.xml boh/marker_definition.xml boh/markers_set.xml boh/samples_container.xml boh/sequencing_data_sample.xml boh/study.xml boh/unauthorized_access.py boh/vessels_collection.xml |
| diffstat | 21 files changed, 2528 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/biosample.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,247 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/birth_data.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,82 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/data_collection.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,125 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/data_object.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,111 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/data_sample.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,166 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/device.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,129 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/diagnosis.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,79 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/enrollment.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,108 @@ +<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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/group.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,75 @@ +<tool id="vl_import_group" name="VLI.group"> + <description>Create a new group 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=$input1 + --ofile=$output1 + --loglevel=$__app__.config.vl_loglevel + --logfile=${logfile} + group + #if str($group_label) != '' + --group=$group_label + #end if + </command> + + <inputs> + <param format="tabular" name="input1" type="data" + label="A tabular dataset with the following columns ..."/> + + <param name="group_label" size="40" type="text" + value="" + label="New group label"/> + + <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="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> + <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 create a new group of individuals from a file with the following columns:: + + study label individual + foo I0000 V06C59B915C0FD47DABE6AE02C731780AF + foo I0001 V0B718B77691B145BFA8901FCCF6B37998 + ... + +where the column study is optional (it can be provided via the +group_label param). Labels should be unique within the file and the +individual field should contain VIDs of existing (within omero/vl) +Individual objects. + </help> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/illumina_bead_chip_measures.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,127 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/importer.py Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,7 @@ +# BEGIN_COPYRIGHT +# END_COPYRIGHT + +import sys +from bl.vl.app.importer.main import main + +main(sys.argv[1:])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/individual.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,99 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/laneslot.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,127 @@ +<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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/marker_alignment.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,140 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/marker_definition.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,119 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/markers_set.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,102 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/samples_container.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,287 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/sequencing_data_sample.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,198 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/study.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,83 @@ +<tool id="vl_import_study" name="VLI.study"> + <description>import study 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 $blocking_validation + --blocking-validator + #end if + study + </command> + + <inputs> + <param format="tabular" name="input" type="data" + label="A tabular dataset with the following columns ..."/> + + <!-- ************************************************** --> + <param name="blocking_validation" type="boolean" checked="false" + label="Blocking validation" + help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> + + <conditional name="wait_for_trigger"> + <param name="enable_trigger" type="boolean" checked="false" + label="Wait for another tool to end before running this tool"/> + <when value="true"> + <param format="txt" name="trigger_file" type="data" + label="Select the LOG file that will be used as trigger"/> + </when> + </conditional> + + <conditional name="advanced_configuration"> + <param name="configuration_level" type="select" + label="Configuration level"> + <option value="default" selected="true">Default configuration</option> + <option value="advanced">Advanced configuration</option> + </param> + <when value="advanced"> + <param name="vl_host" size="40" type="text" + value="localhost" + label="Omero/VL host"/> + <param name="vl_user" size="20" type="text" + value="root" + label="Omero/VL user"/> + <param name="vl_passwd" size="20" type="text" + value="What_Me_worry?" + label="Omero/VL passwd"/> + </when> + <when/> + </conditional> + </inputs> + + <outputs> + <data format="tabular" name="output" label="${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 study definitions defined by the following +tab-separated columns. A typical file will look like the following:: + + label description + BSTUDY A basically empty description of BSTUDY + CSTUDY A basically empty description of CSTUDY + .... + </help> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/unauthorized_access.py Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,6 @@ +# BEGIN_COPYRIGHT +# END_COPYRIGHT + +import sys + +sys.exit("You are not authorized to use this tool")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boh/vessels_collection.xml Thu Sep 22 08:33:51 2016 -0400 @@ -0,0 +1,111 @@ +<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>