diff --git a/manifest b/manifest index 11fd0d6..fe7eb44 100644 --- a/manifest +++ b/manifest @@ -9,7 +9,7 @@ description=Normalizes the median fluorescence intensity (MFI) values in a raw p documentationUrl=https://genepattern.github.io/tfsites.DefineTfSites/v1/ fileFormat= job.cpuCount= -job.docker.image=genepattern/tfsites\:0.9 +job.docker.image=genepattern/tfsites\:0.10 job.memory= job.walltime= language=any @@ -18,7 +18,7 @@ os=any p1_MODE=IN p1_TYPE=FILE p1_default_value= -p1_description=Input file containing the raw PBM dataset. This file is the output of a protein-binding microarray experiment obtained from uniPROBE. +p1_description=File containing the raw PBM dataset. This file is the output of a protein-binding microarray experiment obtained from uniPROBE. p1_fileFormat=.tsv p1_flag= p1_name=raw.PBM.data @@ -28,6 +28,7 @@ p1_prefix= p1_prefix_when_specified= p1_type=java.io.File p1_value= + p2_MODE= p2_TYPE=TEXT p2_default_value=NNGGAWNN @@ -41,10 +42,11 @@ 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 forward DNA sequence in the input PBM file (1-indexed, 1 is the first column). +p3_description=Number of the column containing the forward DNA sequence in the raw PBM file (1-indexed, 1 is the first column). p3_fileFormat= p3_flag= p3_name=column.of.PBM.k-mers @@ -58,7 +60,7 @@ p3_value= p4_MODE= p4_TYPE=Integer p4_default_value=4 -p4_description=Number of the column containing the MFI signal in the input PBM file (1-indexed, 1 is the first column). +p4_description=Number of the column containing the median fluorescence intensity (MFI) signal in the raw PBM file (1-indexed, 1 is the first column). p4_fileFormat= p4_flag= p4_name=column.of.PBM.MFI @@ -100,7 +102,7 @@ p6_value=FALSE\=FALSE;TRUE\=TRUE p7_MODE= p7_TYPE=TEXT p7_default_value=FALSE -p7_description=If True, only report k-mers abiding by the IUPAC definition. If False, report all k-mers. +p7_description=If True, only report k-mers abiding by the binding site definition. If False, report all k-mers. p7_fileFormat= p7_flag= p7_name=report.sites.only @@ -114,7 +116,7 @@ p7_value=FALSE\=FALSE;TRUE\=TRUE p8_MODE= p8_TYPE=TEXT p8_default_value=FALSE -p8_description=If True, normalize the data so the minimum affinity value is set to 0.001. The normalized affinity values will range between 0.001 and 1.0. If False, the values will range between 0 and 1.0. +p8_description=If True, enforce the relative affinities to range between 0 and 1. If False, the original range of the relative affinities will remain the same. p8_fileFormat= p8_flag= p8_name=enforce.minimum.relative.affinity @@ -128,7 +130,7 @@ p8_value=FALSE\=FALSE;TRUE\=TRUE p9_MODE= p9_TYPE=TEXT p9_default_value=.aff-histograms.png -p9_description=Name of the output graph containing 3 histogram plots of the normalized affinity values. +p9_description=Name of the output graph containing 3 histogram plots of the relative affinity values. p9_fileFormat= p9_flag= p9_name=histograms.of.relative.affinity.output.filename