Mercurial > repos > ric > test
changeset 13:5ceb7668e259 draft
Deleted selected files
| author | ric |
|---|---|
| date | Thu, 22 Sep 2016 08:37:55 -0400 |
| parents | 8fdf5996c0fb |
| children | b764aabef6f0 |
| files | boh/importer.py boh/individual.xml boh/laneslot.xml boh/marker_alignment.xml boh/marker_definition.xml |
| diffstat | 5 files changed, 0 insertions(+), 492 deletions(-) [+] |
line wrap: on
line diff
--- a/boh/importer.py Thu Sep 22 08:37:42 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -# BEGIN_COPYRIGHT -# END_COPYRIGHT - -import sys -from bl.vl.app.importer.main import main - -main(sys.argv[1:])
--- a/boh/individual.xml Thu Sep 22 08:37:42 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,99 +0,0 @@ -<tool id="vl_import_individual" name="VLI.individual"> - <description>import individual definitions within omero/vl</description> - <command interpreter="python"> - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --ofile=$output - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=$logfile - #if $blocking_validation - --blocking-validator - #end if - individual - #if str($study) != 'use_provided' - --study $study - #end if - </command> - - <inputs> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records will provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output" label="${tool.name}.mapping"/> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -Will import a stream of new individual definitions defined by the -following columns:: - - label gender father mother - id2 male id4 id5 - id3 female None None - .... - -It is not possible to import the same individual twice: the related -file rows will be noisily ignored. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- a/boh/laneslot.xml Thu Sep 22 08:37:42 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,127 +0,0 @@ -<tool id="vl_import_laneslot" name="VLI.laneslot"> - <description>import LaneSlot definitions within omero.biobank</description> - <command interpreter="python"> - importer.py - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=${in_file} - --ofile=${out_file} - --report_file=${report_file} - --loglevel=$__app__.config.vl_loglevel - --logfile=${log_file} - #if $blocking_validation - --blocking-validator - #end if - laneslot - #if str($study) != 'use_provided' - --study=${study} - #end if - #if str($source_type) != 'use_provided' - --source_type=${source_type} - #end if - #if str($content) != 'use_provided' - --content=${content} - #end if - </command> - - <inputs> - <param format="tabular" name="in_file" type="data" - label="A tabular dataset with the following columns..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="source_type" type="select" - label="Type of the source object" - help="Choose from the legal types. Seel below."> - <option value="use_provided" selected="true"> - Records provide source type - </option> - <option value="Tube">Tube</option> - <option value="PlateWell">PlateWell</option> - <option value="Individual">Individual</option> - </param> - - <param name="content" type="select" - label="Type of content" - help="Choose from the legal types. See below."> - <option value="use_provided" selected="true"> - Records provide content type - </option> - <option value="DNA">DNA</option> - <option value="RNA">RNA</option> - </param> - - <!-- ************************************************** --> - <param name="blocking_validation" type="boolean" checked="false" - label="Blocking validation" - help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/> - - <conditional name="wait_for_trigger"> - <param name="enable_trigger" type="boolean" checked="false" - label="Wait for another tool to end before running this tool"/> - <when value="true"> - <param format="txt" name="trigger_file" type="data" - label="Select the LOG file that will be used as trigger"/> - </when> - </conditional> - - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What? Me_worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="out_file" label="${tool.name}.mapping"/> - <data format="tabular" name="report_file" label="${tool.name}.report"/> - <data format="txt" name="log_file" label="${tool.name}.logfile"/> - </outputs> - - <help> -A lane slot record will have the following fields:: - - lane tag content source - V123411 ATCACG DNA V4512415 - V123411 CGATGT DNA V1415512 - V412511 DNA V1909012 - V661251 TGACCA DNA V1123111 - V661251 CTTGTA DNA V1211141 - .... - -the content column can be option if passed as script's input value, -tag column is optional too. - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool> \ No newline at end of file
--- a/boh/marker_alignment.xml Thu Sep 22 08:37:42 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,140 +0,0 @@ -<tool id="vl_import_marker_alignment" name="VLI.marker_alignment"> - <description>import marker aligments within omero/vl</description> - <command interpreter="python"> - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input - --report_file=$report - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - marker_alignment - #if str($study) != 'use_provided' - --study ${study} - #end if - #if str($ref_genome) - --ref-genome ${reg_genome} - #end if - #if str($message) - --message ${message} - #end if - </command> - - <inputs> - <!-- use a special format to automatically pick up the ref-gen --> - <param format="tabular" name="input" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See help below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <conditional name="genomeSource"> - <param name="refGenomeSource" - type="select" - label="Will you select a reference genome from your history - or use a built-in index?"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select a reference genome"> - <options from_data_table="libbwa_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" - format="fasta" metadata_name="dbkey" - label="Select a reference from history" /> - </when> - </conditional> - <conditional name="paired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param name="input1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" /> - </when> - <when value="paired"> - <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" /> - <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" /> - </when> - </conditional> - - <param name="source" size="40" type="text" value="" - label="source"/> - <param name="context" size="40" type="text" value="" - label="context"/> - <param name="release" size="40" type="text" value="" - label="release"/> - - - <!-- ************************************************** --> - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="report" label="${tool.name}.report"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -Will read in a tsv file with the following columns:: - - marker_vid ref_genome chromosome pos strand allele copies - V0909090 hg18 10 82938938 True A 1 - V0909091 hg18 1 82938999 True A 2 - V0909092 hg18 1 82938938 True B 2 - ... - -Since pos is relative to 5', if the marker has been aligned on the -other strand, it is the responsibility of the aligner app to report -the actual distance from 5', while, at the same time, registering that -the SNP has actually been aligned on the other strand. - -The chromosome field is an integer field with values in the [1, 26] -range, with 23-26 representing, respectively, the X chromosome, the Y -chromosome, the pseudoautosomal regions (XY) and the mitochondrial DNA -(MT). - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>
--- a/boh/marker_definition.xml Thu Sep 22 08:37:42 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,119 +0,0 @@ -<tool id="vl_import_marker_definition" name="VLI.marker_definition"> - <description>import Marker definitions within omero/vl</description> - <command interpreter="python"> - #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py - #else #unauthorized_access.py - #end if - #if $advanced_configuration.configuration_level == 'advanced' - --host=$advanced_configuration.vl_host - --user=$advanced_configuration.vl_user - --passwd=$advanced_configuration.vl_passwd - #end if - --operator=galaxy - --ifile=$input1 - --ofile=$output1 - --loglevel=$__app__.config.vl_loglevel - --logfile=${logfile} - marker_definition - #if str($study) != 'use_provided' - --study ${study} - #end if - --source ${source} - --context ${context} - --release ${release} - --ref-genome ${ref_genome} - --dbsnp-build ${dbsnp_build} - </command> - - <inputs> - <param format="tabular" name="input1" type="data" - label="A tabular dataset with the following columns ..."/> - - <param name="study" type="select" label="Context study" - help="Choose from the already defined studies. See help below."> - <options from_parameter="tool.app.known_studies" - transform_lines="[ "%s%s%s:%s" - % ( l[0], self.separator, l[0], l[1][:40] ) - for l in obj ]"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <filter type="sort_by" column="0"/> - <filter type="add_value" name="Records provide study labels" - value="use_provided" index="0"/> - </options> - </param> - - <param name="source" size="40" type="text" value="" - optional="false" - label="source"/> - <param name="context" size="40" type="text" value="" - optional="false" - label="context"/> - <param name="release" size="40" type="text" value="" - optional="false" - label="release"/> - <param name="ref_genome" size="40" type="text" value="" - optional="false" - label="reference genome"/> - <param name="dbsnp_build" size="40" type="integer" value="0" - optional="false" - label="dbSNP build"/> - - - <!-- ************************************************** --> - <conditional name="advanced_configuration"> - <param name="configuration_level" type="select" - label="Configuration level"> - <option value="default" selected="true">Default configuration</option> - <option value="advanced">Advanced configuration</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="vl_host" size="40" type="text" value="localhost" - label="Omero/VL host"/> - <param name="vl_user" size="20" type="text" value="root" - label="Omero/VL user"/> - <param name="vl_passwd" size="20" type="text" value="What?Me worry?" - label="Omero/VL passwd"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output1" label="${tool.name}.mapping"/> - <data format="txt" name="logfile" label="${tool.name}.logfile"/> - </outputs> - - <help> -Will read in a tsv file with the following columns:: - - label rs_label mask strand allele_a allele_b - SNP_A-1780419 rs6576700 <lflank/>[A/G]<rflank/> TOP A G - ... - -Where label is supposed to be the unique label for this marker in the -(source, context, release) context, rs_label is the dbSNP db label for -this snp (it could be the string ``None`` if not defined or not -known). The column mask contains the SNP definition. The strand column -could either be the actual 'illumina style' strand used to define the -alleles in the alleles columns, or the string 'None', which means that -the alleles in the allele column are defined wrt the mask in the -mask column. - -It will, for each row, convert the mask to the TOP strand following -Illumina conventions and then save a record for it in VL. The saved -tuple is (source, context, release, label, rs_label, TOP_mask). There -are no collision controls. - -It will output a a tsv file with the following columns:: - - study label type vid - ASTUDY SNP_A-xxx Marker V000002222 - ... - </help> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - -</tool>