Mercurial > repos > davidecangelosi > pipe_t
changeset 25:46cb147d53df draft
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 5e4b34d455815432f2e4318721ea71c5d2c840dd
| author | davidecangelosi |
|---|---|
| date | Fri, 31 May 2019 08:08:04 -0400 |
| parents | 6ae13912ab03 |
| children | f008adc272a2 |
| files | README.md |
| diffstat | 1 files changed, 32 insertions(+), 0 deletions(-) [+] |
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--- a/README.md Wed May 29 07:32:50 2019 -0400 +++ b/README.md Fri May 31 08:08:04 2019 -0400 @@ -116,6 +116,38 @@ - A List collection of tab-separated text files containing the resulting data of the RT-qPCR experiment (ListOfFile) - A tab-separated text file associating each filename in ListOfFile with a treatment group (FileTreatment). +File formats must be carefully checked before starting uploading the files in Galaxy. +Here, we list some hints about the fileTreatment file format +1. fileTreatment must be a tab-delimited txt file. +2. fileTreatment must have only two columns named sampleName and Treatment. +3. Be sure that sampleName matches the name and the extension of the files in ListOfFile +4. Omit any special symbol when you specify a sampleName or a Treatment. + + +Here, we list some hints about the ListOfFile list format: +1. Each file in ListOfFile must be a tab-separated text file. +2. Use the dot as decimal separator. +3. Be sure that no special symbol was introduced in the files. +4. Feature and column names must be the same in all input files +5. Each file in ListOfFile must refer to one sample. +6. Check that the feature type is specified as Target or Endogenous Control. +7. SDS and EDS are the only formats with a header in the first rows of the file. PIPE-T automatically discard these header rows before parsing the content of these files. For this reason, the first column of the columns row must start by the symbol # for a SDS file and by the word Well for a EDS file. +8. Be sure that each file contains at least the following column names: + - For format EDS: EXPFAIL, Target Name, Well Position, and CT, + - For format plain: flag as 4th column, feature as 6th column, type as 7th column, position as 3th column, and Ct as 8th column, + - For format SDS: Omit, Detector, Task, and Avg Ct, + - For format LightCycler: Name, Pos, and Cp, + - For format CFX: Content, Well, Cq Mean, + - For format OpenArray: ThroughHole.Outlier, Assay.Assay.ID, Assay.Assay.Type, ThroughHole.Address, and ThroughHole.Ct, + - For format BioMark: Call, Name 1, ID, and Value. +9. Be sure that flag of all features is one of the following values: + - For format EDS: Y or N, + - For format plain: Flagged or Passed, + - For format SDS: TRUE or FALSE, + - For format LightCycler: Y or N, + - For format CFX: Y or N, + - For format OpenArray: TRUE or FALSE, + - For format BioMark: Fail or Pass. ##### Output One single execution of PIPE-T produces the following output files: