Mercurial > repos > ric > test
changeset 12:8fdf5996c0fb draft
Deleted selected files
| author | ric |
|---|---|
| date | Thu, 22 Sep 2016 08:37:42 -0400 |
| parents | 015f2dcc2510 |
| children | 5ceb7668e259 |
| files | 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 | 6 files changed, 0 insertions(+), 787 deletions(-) [+] |
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--- a/boh/markers_set.xml Thu Sep 22 08:33:51 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,102 +0,0 @@ -<tool id="vl_import_markers_set" name="VLI.markers_set"> - <description>import Marker definitions within omero/vl</description> - <command interpreter="python"> - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - markers_set - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($label) - --label ${label} - #end if - #if str($maker) != 'use_provided' - --maker ${maker} - #end if - #if str($model) != 'use_provided' - --model ${model} - #end if - #if str($release) - --release ${release} - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See help below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="label" size="40" type="text" value="" - label="label"/> - <param name="maker" size="40" type="text" value="" - label="maker"/> - <param name="model" size="40" type="text" value="" - label="model"/> - <param name="release" size="40" type="text" value="" - label="release"/> - - <!-- ************************************************** --> - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -Will read in a tsv file with the following columns:: - - marker_vid marker_indx allele_flip - V902909090 0 False - V902909091 1 False - V902909092 2 True - ... - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- a/boh/samples_container.xml Thu Sep 22 08:33:51 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,287 +0,0 @@ -<tool id="vl_import_samples_container" name="VLI.samples_container"> - <description>import samples container definitions within omero/vl</description> - <command interpreter="python"> - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - samples_container - #if str($study) != 'use_provided' - --study=${study} - #end if - #if str($container_type_selector.container_type) != 'use_provided' - --container-type=${container_type_selector.container_type} - #if str($container_type_selector.container_type) == 'TiterPlate' - #if str($container_type_selector.plate_shape) != 'use_provided' - --plate-shape=${container_type_selector.plate_shape} - #end if - #elif str($container_type_selector.container_type) == 'FlowCell' - #if str($container_type_selector.flow_cell_slots) != 'use_provided' - --number-of-slots=${container_type_selector.flow_cell_slots} - #end if - #elif str($container_type_selector.container_type) == 'IlluminaArrayOfArrays' - #if str($container_type_selector.ill_shape) != 'use_provided' - --plate-shape=${container_type_selector.ill_shape} - #end if - #if str($container_type_selector.ill_slots) != 'use_provided' - --number_of_slots=${container_type_selector.ill_slots} - #end if - #if str($container_type_selector.array_type) != 'use_provided' - --illumina-array-type=${container_type_selector.array_type} - #end if - #if str($container_type_selector.array_class) != 'use_provided' - --illumina-array-class=${container_type_selector.array_class} - #end if - #if str($container_type_selector.assay_type) != 'use_provided' - --illumina-assay-type=${container_type_selector.assay_type} - #end if - #end if - #end if - #if str($container_status) != 'use_provided' - --container-status=${container_status} - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <conditional name="container_type_selector"> - <param name="container_type" type="select" label="Container type" - help="Choose from the following container types"> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="TiterPlate">TiterPlate</option> - <option value="FlowCell">Flow Cell</option> - <option value="Lane">Lane</option> - <option value="IlluminaArrayOfArrays">IlluminaArrayOfArrays</option> - </param> - <when value="TiterPlate"> - <param name="plate_shape" type="select" label="Titer Plate's shape" - help="Choose from the following shapes"> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="8x12">8 rows x 12 columns</option> - <option value="32x48">32 rows x 48 columns</option> - </param> - </when> - <when value="FlowCell"> - <param name="flow_cell_slots" type="select" label="Flow Cell slots" - help="Choose from the following list"> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="8">8</option> - </param> - </when> - <when value="IlluminaArrayOfArrays"> - <param name="ill_shape" type="select" label="IlluminArrayOfArrays shape" - help="Choose from the following shapes"> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="6x2">6 rows x 2 columns</option> - <option value="2x6">2 rows x 6 columns</option> - </param> - <param name="ill_slots" type="select" label="IlluminaArrayOfArrays slots" - help="Choose from the following list"> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="12">12</option> - </param> - <param name="array_type" type="select" label="Illumina Array of Arrays type" - help="choose from the following list"> - <options from_parameter="tool.app.known_illumina_array_of_arrays_type" - transform_lines="[ "%s%s%s" - % (o[1], self.separator, o[1]) - for o in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide array type" - value="use_provided" index="0"/> - </options> - </param> - <param name="array_class" type="select" label="Illumina Array of Arrays class" - help="choose from the following list"> - <options from_parameter="tool.app.known_illumina_array_of_arrays_class" - transform_lines="[ "%s%s%s" - % (o[1], self.separator, o[1]) - for o in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide array class" - value="use_provided" index="0"/> - </options> - </param> - <param name="assay_type" type="select" label="Illumina Array of Arrays Assay type" - help="choose from the following list"> - <options from_parameter="tool.app.known_illumina_array_of_arrays_assay_type" - transform_lines="[ "%s%s%s" - % (o[1], self.separator, o[1]) - for o in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide array assay type" - value="use_provided" index="0"/> - </options> - </param> - </when> - </conditional> - - <param name="container_status" type="select" label="Container status" - help="Choose from one of the available values. See below."> - <options from_parameter="tool.app.kb.ContainerStatus.__enums__" - transform_lines="[ "%s%s%s" - % (e.enum_label(), - self.separator, - e.enum_label()) - for e in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide plate status" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -A container record will have the following fields:: - - label container_status creation_date - A_CONTAINER USABLE 13/02/2012 - B_CONTAINER INSTOCK 12/01/2001 - C_CONTAINER USABLE 25/04/2012 - .... - -the creation_date column is optional, if not specified current date -will be set as the object's creation date, also the container_status -column can be optional if this values is passed as input parameter. - - -When importing new containers, special fields can be included in the -CSV file depending on the type of the objects that you want to -import. - -For TITER PLATES objects the syntax can be the following:: - - label barcode container_status rows columns - A_TITERPLATE XXYYZZ111 INSTOCK 8 12 - B_TITERPLATE XXYYZZ112 INSTOCK 8 12 - C_TITERPLATE XXYYZZ113 READY 8 12 - .... - -rows and columns values can be optional if these values are passed as -input parameters, barcode column is optional. - -For ILLUMINA ARRAY OF ARRAYS objects the syntax can be the following:: - - label barcode container_status rows columns illumina_array_type illumina_array_class illumina_assay_type - A_ILLARRAY XXYYZZ111 INSTOCK 4 2 BeadChip_12x1Q Slide Infinium_HD - B_ILLARRAY XXYYZZ112 INSTOCK 4 2 BeadChip_12x1Q Slide Infinium_HD - C_ILLARRAY XXYYZZ113 INSTOCK 4 2 BeadChip_12x1Q Slide Infinium_HD - -rows, columns, illumina_array_type, illumina_array_class and illumina_assay_type -can be optional if these values are passed as input parameters, barcode column -is optional. - -For FLOW CELL objects the syntax can be the following:: - - label barcode container_status number_of_slots - A_FLOWCELL XXYYZZ221 INSTOCK 8 - B_FLOWCELL XXYYZZ222 INSTOCK 8 - C_FLOWCELL XXYYZZ223 INSTOCK 8 - .... - -number_of_slots column can be optional if this value is passed as -input paramter, barcode column is optional. - -For LANE objects the syntax can be the following:: - - flow_cell slot container_status - V112441441 1 INSTOCK - V112441441 2 INSTOCK - V112441441 3 INSTOCK - V351145519 1 INSTOCK - V351145519 2 INSTOCK - .... - -for Lane objects, no label column has to be provided, the importer -will automatically calculate the labels for each imported object. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- a/boh/sequencing_data_sample.xml Thu Sep 22 08:33:51 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,198 +0,0 @@ -<tool id="vl_import_seq_data_sample" name="VLI.seq_data_sample"> - <description> - Import sequencing related DataSample definitions within omero/vl - </description> - <command interpreter="python"> - importer.py - --operator=galaxy - --ifile=${input} - --ofile=${output} - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - seq_data_sample - #if str($study) != 'use_provided' - --study=${study} - #end if - #if str($source_type) != 'use_provided' - --source-type=${source_type} - #end if - #if str($seq_dsample_type) != 'use_provided' - --seq-dsample-type=${seq_dsample_type} - #end if - #if str($dsample_status) != 'use_provided' - --status=${dsample_status} - #end if - #if str($device) != 'use_provided' - --device=${device} - #end if - #if str($history) != 'None' - --history=${history} - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="source_type" type="select" - label="Type of the source" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="FlowCell">FlowCell</option> - <option value="SequencerOutput"> - SequencerOutput - </option> - <option value="RawSeqDataSample"> - RawSeqDataSample - </option> - </param> - - <!-- Choose the device after the type selection, SequencerOutput - will required an HardwareDevice, RawSeqDataSample and SeqDataSample - will required a SoftwareDevice. If the "use provided" is selected, - load a generic Device select list --> - <param name="seq_dsample_type" type="select" - label="Type of the DataSample" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="SequencerOutput"> - SequencerOutput - </option> - <option value="RawSeqDataSample"> - RawSeqDataSample - </option> - <option value="SeqDataSample"> - SeqDataSample - </option> - </param> - - <param name="dsample_status" type="select" label="DataSample status" - help="Choose from one of the available values. See below."> - <options from_parameter="tool.app.known_data_sample_status" - transform_lines="[ "%s%s%s" - % (l[1], self.separator, l[1]) - for l in obj ]"> - <column name="value" index="1"/> - <column name="name" index="0"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide status" - value="use_provided" index="0"/> - </options> - </param> - - <param name="device" type="select" label="device" - help="Choose from the already defined devices. See below."> - <options from_parameter="tool.app.known_devices" - transform_lines = "[ "%s%s%s" - % ( l[0], self.separator, l[1]) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="1"/> - <filter type="add_value" name="Records provide device ids" - value="use_provided" index="0"/> - </options> - </param> - - <param format="txt" name="history" type="data" optional="true" - label="Objects history" - help="Galaxy history in JSON format, history will be shared among all objects"/> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What? Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -Will read a tsv file with the following columns:: - - study label source source_type seq_dsample_type status device - FOOBAR seq_out_1 V012141 FlowCell SequencerOutput USABLE V123141 - FOOBAR seq_out_2 V012141 FlowCell SequencerOutput USABLE V123141 - FOOBAR seq_out_3 V1AD124 FlowCell SequencerOutput USABLE V123141 - ... - -where - * seq_dsample_type can assume one of the following values: SequencerOutput, RawSeqDataSample, SeqDataSample - * source_type can assume one of the following values: FlowCell, SequencerOutput, RawSeqDataSample - -study, source_type, seq_dsample_type, status and device columns can be -overwritten by using command line options. - -A special case of the previous file is when seq_dsample_type is -SeqDataSample, in this case a mandatory sample column is required, -this column has to contain IDs of Tube objects. -The file will look like this - - study label source source_type seq_dsample_type status device sample - FOOBAR seq_dsample_1 V041241 SequencerOutput SeqDataSample USABLE VBB2351 V124AA41 - FOOBAR seq_dsample_2 V051561 SequencerOutput SeqDataSample USABLE VBB2351 V4151AAE - FOOBAR seq_dsample_3 V151561 SequencerOutput SeqDataSample USABLE VBB2351 V15199CD - ... - -A file containing ax export of the Galaxy history that produced the -data that are going to be imported can be passed as input parameter, -history details must represented as a string serialized in JSON -format. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- a/boh/study.xml Thu Sep 22 08:33:51 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -<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>
--- a/boh/unauthorized_access.py Thu Sep 22 08:33:51 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -# BEGIN_COPYRIGHT -# END_COPYRIGHT - -import sys - -sys.exit("You are not authorized to use this tool")
--- a/boh/vessels_collection.xml Thu Sep 22 08:33:51 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,111 +0,0 @@ -<tool id="vl_import_vessels_collection" name="VLI.vessels_collection"> - <description>import VesselsCollection definitions within omero/vl</description> - <command interpreter="python"> - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - vessels_collection - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($vessel_type) != 'use_provided' - --vessel_type=${vessel_type} - #end if - #if str($label) - --label=${label} - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="label" size="20" type="text" value="" - label="collection label"/> - - <param name="vessel_type" type="select" - label="Type of the source" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided</option> - <option value="Vessel">Vessel</option> - <option value="TiterPlate">TiterPlate</option> - </param> - - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What? Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -TODO: add doc here... - </help> - - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>