comparison README.md @ 25:46cb147d53df draft

planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 5e4b34d455815432f2e4318721ea71c5d2c840dd

24:6ae13912ab03

##### Input
To start any PIPE-T execution, users must upload two types of input files: 
- 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). 


##### Output
One single execution of PIPE-T produces the following output files: 
- A tab-separated text file containing the raw Ct values for every samples and transcript 
- A PNG file showing the distribution of the Ct values of every samples obtained after the Ct filtering and categorization step visualized as sequence of boxplots.

25:46cb147d53df

##### Input
To start any PIPE-T execution, users must upload two types of input files: 
- 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: 
- A tab-separated text file containing the raw Ct values for every samples and transcript 
- A PNG file showing the distribution of the Ct values of every samples obtained after the Ct filtering and categorization step visualized as sequence of boxplots.