<commit_before>#
# Define basic display information
#
name     : Identify Differential Expression using Cuffdiff

tooltip  : |
    This method is allowed to identify differential expression using cuffdiff.
screenshots :
    []

#
# Define the set of other narrative methods that should be suggested to the user.
#
method-suggestions :
    related :
        []
    next :
        []


#
# Configure the display and description of the parameters
#
parameters :
  rnaseq_exp_details :
    ui-name : |
      RNASeq Experiment Name
    short-hint : |
      Specify the RNASeq Experiment Name
  output_obj_name :
    ui-name : |
      Cuffdiff output
    short-hint : |
      Provide the name of cuffdiff output
  num-threads :
    ui-name : |
      Number of  threads
    short-hint : |
      Number of  threads to align reads. The default is 1.
  min-alignment-count :
    ui-name : |
      Minimum Count of Alignment
    short-hint : |
      Minimum number of alignments in a locus to conduct significant changes in the locus between samples. The default is 10. 
  time-series :
    ui-name : |
      Time Series
    short-hint : |
       Analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. 
  multi-read-correct :
    ui-name : |
      Multi Read Correct
    short-hint : |
      To provide more accurately weight reads mapping to multiple locations in the genome. 
  labels  :
    ui-name : |
      Labels
    short-hint : |
      Specify a label for each sample which will be included in various cuffdiff output files.
  library-type  :
    ui-name : |
      Library Types
    short-hint : |
      Select the library type.
  library-norm-method :
    ui-name : |
      Library Normalization Method
    short-hint : |
      Select the library normalization method.<commit_msg> labels changed to condition labels in yaml<commit_after>#
# Define basic display information
#
name     : Identify Differential Expression using Cuffdiff

tooltip  : |
    This method is allowed to identify differential expression using cuffdiff.
screenshots :
    []

#
# Define the set of other narrative methods that should be suggested to the user.
#
method-suggestions :
    related :
        []
    next :
        []


#
# Configure the display and description of the parameters
#
parameters :
  rnaseq_exp_details :
    ui-name : |
      RNASeq Experiment Name
    short-hint : |
      Specify the RNASeq Experiment Name
  output_obj_name :
    ui-name : |
      Cuffdiff output
    short-hint : |
      Provide the name of cuffdiff output
  num-threads :
    ui-name : |
      Number of  threads
    short-hint : |
      Number of  threads to align reads. The default is 1.
  min-alignment-count :
    ui-name : |
      Minimum Count of Alignment
    short-hint : |
      Minimum number of alignments in a locus to conduct significant changes in the locus between samples. The default is 10. 
  time-series :
    ui-name : |
      Time Series
    short-hint : |
       Analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. 
  multi-read-correct :
    ui-name : |
      Multi Read Correct
    short-hint : |
      To provide more accurately weight reads mapping to multiple locations in the genome. 
  labels  :
    ui-name : |
      Condition Labels
    short-hint : |
      Specify a label for each sample which will be included in various cuffdiff output files.
  library-type  :
    ui-name : |
      Library Types
    short-hint : |
      Select the library type.
  library-norm-method :
    ui-name : |
      Library Normalization Method
    short-hint : |
      Select the library normalization method.
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