Round 2 ov Nov updates, 2 new parameters added and flags for others c…

…hanged for no good reason

manifest

@@ -3,14 +3,14 @@
 JVMLevel=
 LSID=urn\:lsid\:8080.gpserver.ip-172-31-26-71.ip-172-31-26-71.ec2.internal\:genepatternmodules\:706\:1
 author=Joe Solvason
-commandLine=python /build/tfsites-webportal/01-defineTfSites/01-defineTfSites.py -r <raw.data> -b <core.binding.site.definition> -k <DNA.sequence.column> -v <affinity.column>  -p <header.present>          
+commandLine=python /build/tfsites-webportal/01-normalizeTfDnaAffinityData/01-normalizeTfDnaAffinityData.py -r <raw.data> -b <core.binding.site.definition> -d <DNA.sequence.column> -a <affinity.column>  -p <header.present> -S <output.image.as.svg> -o <output.filename.prefix>         
 # -t <reference.relative.affinity.table.output.filename>
 cpuType=any
 description=Normalizes the median fluorescence intensity (MFI) values in a raw protein-binding microarray (PBM) data file for a transcription factor of interest. The k-mer with the maximum MFI that conforms to the IUPAC definition of a binding site is normalized to 1.0 and all other k-mers are normalized relative to that MFI value. 
 documentationUrl=https://genepattern.github.io/tfsites.NormalizeTfDnaAffinityData/v2/
 fileFormat=
 job.cpuCount=
-job.docker.image=genepattern/tfsites\:0.11
+job.docker.image=genepattern/tfsites\:0.12
 job.memory=
 job.walltime=
 language=any
@@ -30,42 +30,43 @@ p1_prefix_when_specified=
 p1_type=java.io.File
 p1_value=
 
+
 p2_MODE=
 p2_TYPE=TEXT
-p2_default_value=NNGGAWNN
+p2_default_value=relative-aff-table_site_<core.binding.site.definition>
 p2_description=IUPAC definition of the core transcription factor binding site(see <a href="https://www.bioinformatics.org/sms/iupac.html">here</a>). The length of the IUPAC definition should be the same length k as the k-mers in the raw affinity file.
 p2_fileFormat=
 p2_flag=
-p2_name=core.binding.site.definition
+p2_name=output.filename.prefix
 p2_numValues=0..1
 p2_optional=
 p2_prefix=
 p2_prefix_when_specified=
 p2_type=java.lang.String
 p2_value=
 
+
 p3_MODE=
-p3_TYPE=Integer
-p3_default_value=1
-p3_description=Number of the column containing the DNA sequences in the raw affinity file (1-indexed, 1 is the first column).
+p3_TYPE=TEXT
+p3_default_value=NNGGAWNN
+p3_description=IUPAC definition of the core transcription factor binding site(see <a href="https://www.bioinformatics.org/sms/iupac.html">here</a>). The length of the IUPAC definition should be the same length k as the k-mers in the raw affinity file.
 p3_fileFormat=
 p3_flag=
-p3_name=DNA.sequence.column
-p3_numValues=1..1
+p3_name=core.binding.site.definition
+p3_numValues=0..1
 p3_optional=
 p3_prefix=
 p3_prefix_when_specified=
-p3_type=java.lang.Integer
+p3_type=java.lang.String
 p3_value=
 
-
 p4_MODE=
 p4_TYPE=Integer
-p4_default_value=4
-p4_description=Number of the column containing the raw affinity values in the input file (1-indexed, 1 is the first column).
+p4_default_value=1
+p4_description=Number of the column containing the DNA sequences in the raw affinity file (1-indexed, 1 is the first column).
 p4_fileFormat=
 p4_flag=
-p4_name=affinity.column
+p4_name=DNA.sequence.column
 p4_numValues=1..1
 p4_optional=
 p4_prefix=
@@ -75,18 +76,48 @@ p4_value=
 
 
 p5_MODE=
-p5_TYPE=TEXT
-p5_default_value=FALSE
-p5_description=If True, a header exists in the PBM data file. If False, no header exists.
+p5_TYPE=Integer
+p5_default_value=4
+p5_description=Number of the column containing the raw affinity values in the input file (1-indexed, 1 is the first column).
 p5_fileFormat=
 p5_flag=
-p5_name=header.present
-p5_numValues=0..1
+p5_name=affinity.column
+p5_numValues=1..1
 p5_optional=
 p5_prefix=
 p5_prefix_when_specified=
-p5_type=java.lang.String
-p5_value=FALSE\=FALSE;TRUE\=TRUE
+p5_type=java.lang.Integer
+p5_value=
+
+
+p6_MODE=
+p6_TYPE=TEXT
+p6_default_value=FALSE
+p6_description=If True, a header exists in the PBM data file. If False, no header exists.
+p6_fileFormat=
+p6_flag=
+p6_name=header.present
+p6_numValues=0..1
+p6_optional=
+p6_prefix=
+p6_prefix_when_specified=
+p6_type=java.lang.String
+p6_value=FALSE\=FALSE;TRUE\=TRUE
+
+
+p7_MODE=
+p7_TYPE=TEXT
+p7_default_value=FALSE
+p7_description=If True, a header exists in the PBM data file. If False, no header exists.
+p7_fileFormat=
+p7_flag=
+p7_name=output.image.as.svg
+p7_numValues=0..1
+p7_optional=
+p7_prefix=
+p7_prefix_when_specified=
+p7_type=java.lang.String
+p7_value=FALSE\=FALSE;TRUE\=TRUE
 
 
 #p5_MODE=