source: plugins/base1/se.lu.onk.cgh_dataDumper/cgh_dataDumper.base @ 720

BASEfile
section plugin
uniqueName  onk.lu.se/johans/cghDataDumper/
versionNumber 1.0
name  Export: CGH Data Dumper
descr Export: CGH Data Dumper\r\n\r\nThis plugin exports typical BAC data in a simple format readily accessible for e.g. Excel, CGHExplorer, MeV CGH viewer. This plugin works on a normal base file (matrix mode). Therefore, you might want to join array designs using Virtual array if having different designs before running this plugin.\r\n\r\nExported fields are:\r\nReporterId = BAC clone Id\r\nGeneSymbol = Gene symbols of genes mapped to the BAC clone. Could be bundled using ;\r\nChromosome\r\nCytoBand\r\nStartPosition = Start position in BP for the BAC clone\r\nEndPosition = End position in BP for the BAC clone\r\nM = Log2(ratio)\r\n\r\nObserve, that the CGH formats do require probes to be exported to have a genomic mapping.\r\n\r\nStandard Format:\r\nFormat of header line is the above common columns and then the assays with assay names in the header.\r\n\r\nLite Format:\r\nFormat of header line is reporterId,chromosome,start,stop and then the assays with assay names in the header. NOTE: This format should be compatible with MeV CGH viewer.\r\n\r\nSample Name export:\r\nOnly the sample names are exported into a file. No spot data.\r\n\r\nSample Name and annotation export:\r\nThe sample name and a chosen annotation is exported into a file. No spot data.\r\n\r\nAnnotation statistics:\r\nBy specifying in the appropiate text field below in the format e.g. |ER status|brca_family_status|..| you can get a summary of how many assays has a certain annotation value for each of the specified annotation types\r\n\r\nBED format:\r\nThis creates a format similar to BED format as defined by UCSC and Ensembl. Contains four columns, chr,start,stop,reporterId\r\nYou can use bed files to create your own tracks in e.g. UCSC genome browser.\r\n\r\nSingle file Lite. This creates N number of files corresponding to N number of assays. The file name speciefed as a parameter will be the suffix to the assay name. E.g specifying myfile.txt will create a file for Ca13928 as Ca13928_myfile.txt . The format of the individual files are the Lite format (reporterId, chromosome, start, stop, M).\r\n\r\nComplete annotations to file:\r\nThe annotations for all assays are printed to a file. Blanks are filled with NA\r\n\r\nSelected annotations to file:\r\nOnly selected annotations and their assays are printed to file. Blanks are filled with NA.\r\n\r\nMev + annotations\r\nAn MeV compatible file are printed, together with annotations. [TO BE COMPLETED]\r\n\r\nAnnotation Display dump for selected annotations:\r\nFor annotation display option. Enter selected annotations in the format:\r\n|ER Status|p_brca_family_status|etc..|\r\nThese annotations will be separated and a matrix created with N rows = N samples and for each annotation value type, a column will be made with N rows, where each row entry is 1 (annotation value exists for this assay) or 0, no annotation value.\r\n\r\nParameters:\r\n1. [Optional] Give a valid full file name for the created file.\r\n2. [Optional] Sort the data as well. OBS\! Using the sort option may require you to increase the RAM usage considerably if working with large data sets.\r\n3. Select export mode. Either standard or standard_lite as described above, or format suitable for Agilent CGH-analytics software.\r\n4. Select annotation for sample name and annotation export\r\n5. Define annotation types for annotation statistics in the form |ERstatus|brca_family_status|...|\r\n\r\nEnjoy\!  \r\n
execName  onk.lu.se/johans/cghDataDumper/cgh_dataDumper.pl
geneAverages  0
serialFormat  0
url 
minChannels 2
maxChannels 0
leaveStdin  0
leaveStdout 0
estimatedTime 3600
defaultMaxRam 134217728
usedColumns reporterId\tgeneSymbol\tchromosome\tcytoBand\tstartPosition\tendPosition
usedFields  l2ratio1_2
columns position  valueType name  commonName  options defaultValue  enumOptions removed
%
1 h section   30  cghDataDumperParams   0
13  t filename  [Optional]  Give the export file a specific filename  50  NULL    0
14  e sort  Sort the data as well?  30  TRUE  TRUE\tYes\tFALSE\tNo  0
16  e exportMode  Select export mode  30  standard_lite standard\tStandard format\tagilent\tAgilent CGH-analytics format \tstandard_lite\tStandard Lite\tsampleName\tSample names alone\tsampleName_annotation\tSample names + selected annotation\tannotationStatistics\tAnnotation statistics\tbed\tBED format\tsingleLite\tSingle assay Lite format\tannotationAll\tComplete annotations to file\tannotationSelected\tSelected annotations to file\tMeVannotationAll\tMeV all annotations\tannotationDisplaySelected\tAnnotation display export selected annotations 0
20  n annotationType  Select annotation for sample name - annotation export 30  0   0
21  t annoForStat Define the annotation types to get statistics for as |..|..|  30  NULL    0
22  t yscale  Define y-scale in log 2 ratio 30  NULL    1
23  i min.clones  Define a minimum number of clones required for each chromosome  30  20    1
24  e boxes Select degree of  "prettines" on plot 30  pretty  standard\tStandard\tpretty\tPretty \tsimple\tSimple 1
25  t noiselines  Define if desired 2 "noise lines" in log2(ratio) that will be plotted as dashed 30  NULL    1
26  t highlight Highlight the following clones  100 NULL    1
27  e lines Select if to have lines, dots, or both connecting clones  30  p p\tClones as dots\tb\tClones as dots + lines between clones\tl\tOnly lines between dots 1
28  t assayNameStruct Assay name structure (DO NOT USE %) 30  &1_&2   1
29  t assayGroup  Assay grouping item 30  NULL    1
30  e plotStyle Select co-plotting style  30  0 0\tSide by side horizontal\t1\tOn top of each other horizontal  1
31  t stringDivider Please enter the string divider if coplotting 5 _   1
33  t highlightGene Highlight the following GENES 30  NULL    1
34  e VisualizeSegDup Visualize segmental duplications  30  FALSE TRUE\tYes\tFALSE\tNo  1
35  f qcSegDup  If visualize segDup, enter crosshyb cut off 30  1   1