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changeset 8:231b2478ab7d draft

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Deleted selected files
author ric
date Thu, 22 Sep 2016 09:32:27 -0400
parents 8924f77c59ee
children 8a882207b3bf
files galaxy-tools/biobank/utils/gdoize_ms.xml galaxy-tools/biobank/utils/prepare_illumina_import_inputs.py galaxy-tools/biobank/utils/prepare_illumina_import_inputs.xml
diffstat 3 files changed, 0 insertions(+), 292 deletions(-) [+]
line wrap: on
line diff
--- a/galaxy-tools/biobank/utils/gdoize_ms.xml	Thu Sep 22 09:30:45 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-<tool id="vl_tools_gdoize_ms" name="VLUTILS.gdoize_ms">
-  <description>
-    Build missing GDOs for the selected markers set
-  </description>
-  <requirements>
-    <requirement type="package">py_protobuff_cpp</requirement>
-  </requirements>
-  <command>
-    gdoize_ms
-    --loglevel=$__app__.config.vl_loglevel
-    --logfile=${logfile}
-    #if str($mset_label) != 'select_one'
-      --markers-set-label=$mset_label
-    #end if
-    #if str($study) != 'select_one'
-      --study-label=$study
-    #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
-  </command>
-  <inputs>
-    <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="[ &quot;%s%s%s:%s&quot;
-	                          % ( 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="Select a study"
-		value="select_one" index="0"/>
-      </options>
-    </param>
-    <param name="mset_label" type="select" label="SNP Markers Set"
-	   help="Choose one of the already defined SNP Markers set.">
-      <options from_parameter="tool.app.known_marker_sets"
-	      transform_lines="[ &quot;%s%s%s&quot;
-	                         % (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="Select a SNP markers set"
-		value="select_one" 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="biobank05.crs4.it" 
-	       label="Omero/VL host"/>
-	<param name="vl_user" size="20" type="text" value="galaxy" 
-	       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="txt" name="logfile" label="${tool.name}.log"/>
-  </outputs>
-
-  <help>
-Iterate over all genotype data samples corresponding to the given
-marker set; create a GDO table row for each genotpye data sample that
-does not already have one.
-  </help>
-</tool>
\ No newline at end of file
--- a/galaxy-tools/biobank/utils/prepare_illumina_import_inputs.py	Thu Sep 22 09:30:45 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,155 +0,0 @@
-from bl.core.io.illumina import GenomeStudioSampleSheetReader as gsr
-from bl.vl.utils import LOG_LEVELS, get_logger
-import csv, argparse, sys, re
-
-
-def make_parser():
-    parser = argparse.ArgumentParser('Split GenomeStudio samplesheet in TSV files to import data within OMERO')
-    parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
-    parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
-                        help='logging level', default='INFO')
-    parser.add_argument('--input-file', type=str, required=True,
-                        help='GenomeStudio samplesheet')
-    parser.add_argument('--arrays-out-file', type=str,
-                        help='output file containing IlluminaArrayOfArrays definitions',
-                        default='./array_of_arrays.tsv')
-    parser.add_argument('--bead-chip-out-file', type=str,
-                        help='output file containing IlluminaBeadChipArray definitions',
-                        default='./bead_chip.tsv')
-    parser.add_argument('--array-measure-out-file', type=str,
-                        help='output file containing IlluminaBeadChipMeasure definitions',
-                        default='./array_measure.tsv')
-    parser.add_argument('--array-measures-out-file', type=str,
-                        help='output file containing IlluminaBeadChipMeasures definitions',
-                        default='./array_measures.tsv')
-    parser.add_argument('--study', type=str, required=True,
-                        help='Study label that will be used in the import procedure')
-    return parser
-
-
-def get_assay_type_enum(manifest_file):
-    return manifest_file.strip().replace('.bpm', '').replace('-', '_').replace(' ', '_').upper()
-
-
-def prepare_array_of_arrays_input(barcode, study, elements):
-    ICHIPCORDS_PATTERN = re.compile(r'^r(\d{2})c(\d{2})$', re.IGNORECASE)
-    rows = []
-    cols = []
-    for x in elements:
-        m = re.match(ICHIPCORDS_PATTERN, x['array_label'])
-        rows.append(int(m.groups()[0]))
-        cols.append(int(m.groups()[1]))
-    return {
-        'barcode': barcode,
-        'rows': max(rows),
-        'columns': max(cols),
-        'label': barcode,
-        'study': study,
-    }
-
-
-def barcodes_to_labels(elements, wells_map, strict_mapping, logger):
-    from copy import deepcopy
-
-    mapped_elements = []
-    for e in elements:
-        if e['source'] in wells_map:
-            new_el = deepcopy(e)
-            new_el['source'] = wells_map[e['source']]
-            mapped_elements.append(new_el)
-        else:
-            logger.warning('Unable to map well %s' % e['source'])
-
-    if strict_mapping and len(mapped_elements) < len(elements):
-        msg = 'Mapped %d records of %d' %(len(elements), len(mapped_elements))
-        logger.critical(msg)
-        sys.exit(msg)
-    return mapped_elements
-
-
-def prepare_bead_chip_array_input(array_barcode, assay_type, study, elements):
-    return [{
-        'illumina_array': array_barcode,
-        'label': x['array_label'],
-        'source': x['source'],
-        'bead_chip_assay_type': assay_type,
-        'study': study,
-    } for x in elements]
-
-
-def prepare_bead_chip_measure_input(array_barcode, study, elements,
-                                    device='generic_illumina_scanner',
-                                    status='USABLE'):
-    records = []
-    for channel in ['Grn', 'Red']:
-        records.extend(
-            [
-                {
-                    'label': '%s_%s_%s' % (array_barcode, x['array_label'], channel),
-                    'source': '%s:%s' % (array_barcode, x['array_label']),
-                    'scanner': device,
-                    'status': status,
-                    'study': study,
-                } for x in elements
-            ]
-        )
-    return records
-
-
-def prepare_bead_chip_array_measures_input(array_barcode, study, elements):
-    return [{
-        'study': study,
-        'label': '%s_%s' % (array_barcode, x['array_label']),
-        'red_channel': '%s_%s_Red' % (array_barcode, x['array_label']),
-        'green_channel': '%s_%s_Grn' %(array_barcode, x['array_label']),
-        'source': '%s:%s' % (array_barcode, x['array_label']),
-    } for x in elements]
-
-
-def main(argv):
-    parser = make_parser()
-    args = parser.parse_args(argv)
-
-    logger = get_logger('prepare_illumina_import_inputs', level=args.loglevel,
-                        filename=args.logfile)
-
-    logger.info('Processing file %s', args.input_file)
-    with open(args.input_file) as in_file:
-        reader = gsr(in_file)
-        assay_type = get_assay_type_enum(reader.header['A'])
-        arrays_map = {}
-        for r in reader:
-            arrays_map.setdefault(r['SentrixBarcode_A'], []).append({'source': r['Sample_ID'],
-                                                                     'array_label': r['SentrixPosition_A']})
-        with open(args.arrays_out_file, 'w') as array_file,\
-            open(args.bead_chip_out_file, 'w') as chip_file,\
-            open(args.array_measures_out_file, 'w') as measures_file,\
-            open(args.array_measure_out_file, 'w') as measure_file:
-            arrays_writer = csv.DictWriter(array_file,
-                                           ['study', 'label', 'barcode', 'rows', 'columns'],
-                                           delimiter='\t')
-            arrays_writer.writeheader()
-            chip_writer = csv.DictWriter(chip_file,
-                                         ['study', 'illumina_array', 'label', 'source',
-                                          'bead_chip_assay_type'],
-                                         delimiter='\t')
-            chip_writer.writeheader()
-            measure_writer = csv.DictWriter(measure_file,
-                                            ['study', 'label', 'source', 'scanner', 'status'],
-                                            delimiter='\t')
-            measure_writer.writeheader()
-            measures_writer = csv.DictWriter(measures_file,
-                                             ['study', 'label', 'red_channel', 'green_channel',
-                                              'source'],
-                                             delimiter='\t')
-            measures_writer.writeheader()
-            for k, v in arrays_map.iteritems():
-                arrays_writer.writerow(prepare_array_of_arrays_input(k, args.study, v))
-                chip_writer.writerows(prepare_bead_chip_array_input(k, assay_type, args.study, v))
-                measure_writer.writerows(prepare_bead_chip_measure_input(k, args.study, v))
-                measures_writer.writerows(prepare_bead_chip_array_measures_input(k, args.study, v))
-    logger.info('Job completed')
-
-
-if __name__ == '__main__':
-    main(sys.argv[1:])
\ No newline at end of file
--- a/galaxy-tools/biobank/utils/prepare_illumina_import_inputs.xml	Thu Sep 22 09:30:45 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-<tool id="vl_prepare_illumina_import_inputs"
-      name="VLUTIL.prepare_illumina_import_inputs">
-
-    <description>
-        Prepare inputs file used to import illumina data
-    </description>
-
-    <command interpreter="python">
-        prepare_illumina_import_inputs.py
-        --input-file=${infile}
-        --loglevel=$__app__.config.vl_loglevel
-        --logfile=${log_file}
-        #if str($study) != 'select_study'
-            --study=${study}
-        #end if
-        --arrays-out-file=${arrays_out_file}
-        --bead-chip-out-file=${bead_chip_out_file}
-        --array-measure-out-file=${measure_out_file}
-        --array-measures-out-file=${measures_out_file}
-    </command>
-
-    <inputs>
-        <param format="txt" name="infile" type="data"
-               label="Samplesheet (in TAB-separated format)"/>
-        <param name="study" type="select" label="Study label">
-            <options from_parameter="tool.app.known_studies"
-                    transform_lines="[ &quot;%s%s%s:%s&quot;
-                                      % ( l[0], self.separator, l[0], l[1][:40] )
-                                      for l in obj ]">
-                <column name="name" index="1"/>
-                <column name="value" index="0"/>
-                <filter type="sort_by" column="1"/>
-                <filter type="add_value" name="Select a study"
-                        value="select_study" index="0"/>
-            </options>
-        </param>
-    </inputs>
-
-    <outputs>
-        <data format="tabular" name="arrays_out_file"
-              label="${tool.name}_arrays.tsv"/>
-        <data format="tabular" name="bead_chip_out_file"
-              label="${tool.name}_bead_chips.tsv"/>
-        <data format="tabular" name="measure_out_file"
-              label="${tool.name}_measure.tsv"/>
-        <data format="tabular" name="measures_out_file"
-              label="${tool.name}_measures.tsv"/>
-        <data format="txt" name="log_file"
-              label="${tool.name}.log"/>
-    </outputs>
-
-    <help>
-Prepare file to import IlluminaArrayOfArrays and IlluminaBeadChip objects reading data from a
-GenomeStudio samplesheet
-    </help>
-
-</tool>
\ No newline at end of file