Mercurial > repos > ric > test
changeset 14:b764aabef6f0 draft
Deleted selected files
| author | ric |
|---|---|
| date | Thu, 22 Sep 2016 08:38:04 -0400 |
| parents | 5ceb7668e259 |
| children | 9fc9fc2a958f |
| files | 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 |
| diffstat | 7 files changed, 0 insertions(+), 795 deletions(-) [+] |
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--- a/boh/data_object.xml Thu Sep 22 08:37:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,111 +0,0 @@ -<tool id="vl_import_data_object" name="VLI.data_object"> - <description>import DataObject definitions within omero/vl</description> - <command interpreter="python"> - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - data_object - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($mimetype) != 'use_provided' - --mimetype=${mimetype} - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="mimetype" type="select" - label="mimetype for the data object." - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided</option> - <option value="x-vl/affymetrix-cel">x-vl/affymetrix-cel</option> - </param> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What? Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -Will read in a tsv file with the following columns:: - - study path data_sample mimetype size sha1 - - TEST01 file:/share/fs/v039303.cel V2902 x-vl/affymetrix-cel 39090 E909090 - .... - -Records that point to an unknown data sample will be noisily -ignored. The same will happen to records that have the same path of a -previously seen data_object - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- a/boh/data_sample.xml Thu Sep 22 08:37:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,166 +0,0 @@ -<tool id="vl_import_data_sample" name="VLI.data_sample"> - <description>import DataSample definitions within omero/vl</description> - <command interpreter="python"> - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - data_sample - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($source_type) != 'use_provided' - --source-type=${source_type} - #end if - #if str($device_type) != 'use_provided' - --device-type=${device_type} - #end if - #if str($scanner) != 'use_provided' - --scanner=${scanner} - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="source_type" type="select" - label="Type of the source" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided - </option> - <option value="Individual">Individual</option> - <option value="Tube">Tube</option> - <option value="PlateWell">PlateWell</option> - <option value="DataSample">DataSample</option> - <option value="DataCollectionItem">DataCollectionItem</option> - <option value="IlluminaBeadChipArray">IlluminaBeadChipArray</option> - <option value="IlluminaBeadChipMeasures">IlluminaBeadChipMeasures</option> - </param> - - <param name="device_type" type="select" - label="Type of the device" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided</option> - <option value="Device">Device</option> - <option value="Chip">Chip</option> - <option value="SoftwareProgram">SoftwareProgram</option> - </param> - - <param name="scanner" type="select" label="Scanner used" - help="Choose from the possible scanners. See below."> - <options from_parameter="tool.app.known_scanners" - transform_lines="[ "%s%s%s(%s)" - % ( l[0], self.separator, l[1], l[2]) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="1"/> - <filter type="add_value" name="Records provide scanner ids" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What? Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -Will read in a tsv file with the following columns:: - - study label source device device_type scanner options - ASTUDY foo01 v03909 v9309 Chip v99020 celID=0009099090 - ASTUDY foo02 v03909 v99022 Scanner v99022 conf1=...,conf2=... - .... - -In this example, the first line corresponds to a dataset obtained by -using chip v9309 on scanner v99020, while the second datasample has -been obtained using a technology directly using a scanner, e.g., an -Illumina HiSeq 2000. The '''scanner''' column is there as a -convenience to support a more detailed description of a chip-based -acquisition. - -The general strategy is to decide what data objects should be -instantiated by looking at the chip column and at its corresponding -maker,model,release. - -The optional column '''scanner''', the vid of the scanner device, is -used in cases, such as Affymetrix genotyping, where it is relevant. - -It is also possible to import DataSample(s) that are the results of -processing other DataSample(s). Here is an example:: - - study label source device device_type options - ASTUDY foo01 v03909 v99021 SoftwareProgram conf1=...,conf2=... - ASTUDY foo02 v03909 v99021 SoftwareProgram conf1=...,conf2=... - .... - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- a/boh/device.xml Thu Sep 22 08:37:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,129 +0,0 @@ -<tool id="vl_import_device" name="VLI.device"> - <description>import Device definitions within omero/vl</description> - <command interpreter="python"> - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - device - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($device_type) != 'use_provided' - --device-type=${device_type} - #end if - #if str($maker) - --maker=${maker} - #end if - #if str($model) - --model=${model} - #end if - #if str($release) - --relese=${release} - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="device_type" type="select" - label="type of the device" - help="Choose from the following. See below."> - <option value="use_provided" selected="true"> - Use record provided</option> - <option value="Chip">Chip</option> - <option value="Scanner">Scanner</option> - <option value="SoftwareProgram">SoftwareProgram</option> - <option value="GenotypingProgram">GenotypingProgram</option> - </param> - - <param name="maker" size="40" type="text" value="" label="Device maker"/> - <param name="model" size="40" type="text" value="" label="Device model"/> - <param name="release" size="40" type="text" value="" - label="Device release"/> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -Will read in a tsv file with the following columns:: - - study device_type label barcode maker model release location - BSTUDY Scanner pula01 8989898 Affymetrix GeneChip Scanner 3000 7G Pula bld. 5 - BSTUDY Chip chip001 8329482 Affymetrix Genome-Wide Human SNP Array 6.0 None - -All devices have a type, a label, an optional barcode, a maker, a -model, a release and an optional physical location. In the example -above, in the first line we have defined a scanner, which is -physically located in the building 5 lab in Pula. The second line -defines a chip. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- a/boh/diagnosis.xml Thu Sep 22 08:37:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,79 +0,0 @@ -<tool id="vl_import_diagnosis" name="VLI.diagnosis"> - <description>import diagnosis data within omero/vl</description> - <command interpreter="python"> - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - diagnosis - #if str($study) != 'use_provided' - --study ${study} - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ************************************************** --> - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -Will read in a tsv file with the following columns:: - - study individual timestamp diagnosis - ASTUDY V899 1310057541608 icd10-cm:E10 - ASTUDY V899 1310057541608 icd10-cm:G35 - ASTYDY V1806 1310057541608 exclusion-problem_diagnosis - ... - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- a/boh/enrollment.xml Thu Sep 22 08:37:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,108 +0,0 @@ -<tool id="vl_import_enrollment" name="VLI.enrollment"> - <description>Create new enrollmnents for existing individuals within omero/vl</description> - <command interpreter="python"> - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__) == 1 #importer.py - #else #unauthorized_access.py - #end if - #if str($advanced_configuration.configuration_level) == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - enrollment - #if str($study_label) != 'use_provided' - --study=$study_label - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study_label" type="select" label="Context study" - help="Choose from already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % (l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records will provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -Import of new enrollments related to existing individuals. -An enrollment is characterized by the following fields:: - - source study label - V044DE795E7F9F42FEB9855288CF577A77 xxx id1 - V06C59B915C0FD47DABE6AE02C731780AF xxx id2 - V01654DCFC5BB640C0BB7EE088194E629D xxx id3 - -where source must be the VID of an existing Individual object, study a -label of an existing Study object and label the enrollment code for -the patient in the study. - -The enrollment sub-operation will retrieve the source individual from -the DB, create a new enrollment related to it and output the VIDs of -newly created enrollments. It is not possible to create two -enrollments with the same code related to the same study, nor is it -possible to enroll a patient twice in the same study, even with -different codes. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool> \ No newline at end of file
--- a/boh/group.xml Thu Sep 22 08:37:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,75 +0,0 @@ -<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>
--- a/boh/illumina_bead_chip_measures.xml Thu Sep 22 08:37:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,127 +0,0 @@ -<tool id="vl_import_illumina_bead_chip_measures" name="VLI.illumina_bead_chip_measures"> - <description>import IlluminaBeadChipMeasures definitions within OMERO</description> - <command interpreter="python"> - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=${input} - --ofile=${output} - --report_file=${report} - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - #if $blocking_validation - --blocking-validator - #end if - illumina_bead_chip_measures - #if str($study) != 'use_provided' - --study=${study} - #end if - #if str($source_type) != 'use_provided' - --source_type=${source_type} - #end if - #if str($action_category) != 'use_provided' - --action_category=${action_category} - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="source_type" type="select" - label="Type of the source" - help="Choose from the following source classes. See below."> - <option value="use_provided" selected="true">Use record provided</option> - <option value="IlluminaBeadChipArray">IlluminaBeadChipArray</option> - </param> - - <param name="action_category" type="select" - label="Action category" - help="Choose from the following action categories. See below."> - <options from_parameter="tool.app.known_action_categories" - transform_lines="[ "%s%s%s" - % ( l[1], self.separator, l[1] ) - for l in obj]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide action category" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ********************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="biobank05.crs4.it" - label="OMERO host"/> - <param name="vl_user" size="40" type="text" value="galaxy" - label="OMERO user"/> - <param name="vl_passwd" size="40" type="text" value="What? Me worry?" - label="OMERO password"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -Will read a tsv file with the following columns:: - - study label red_channel green_channel source source_type - ASTUDY CHIP_01_R01C01 V1415151235513 V135135661356161 V351351351551 IlluminaBeadChipArray - ASTUDY CHIP_01_R01C02 V2346262462462 V112395151351623 V135113513223 IlluminaBeadChipArray - ASTUDY CHIP_01_R02C01 V1351362899135 V913977551235981 V100941215192 IlluminaBeadChipArray - -This will create new IlluminaBeadChipMeasures whose labels are defined in the -label column. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>