From ac8f8ed261b7805f426fe58cc9402d5815036b31 Mon Sep 17 00:00:00 2001 From: liefeld Date: Mon, 25 Nov 2024 08:15:09 -0800 Subject: [PATCH] Updates for Nov 2024 --- _paramgroups.json | 22 +++++++++ build.xml | 2 +- manifest | 119 +++++++++++++--------------------------------- paramgroups.json | 27 ----------- 4 files changed, 57 insertions(+), 113 deletions(-) create mode 100644 _paramgroups.json delete mode 100644 paramgroups.json diff --git a/_paramgroups.json b/_paramgroups.json new file mode 100644 index 0000000..c3dd286 --- /dev/null +++ b/_paramgroups.json @@ -0,0 +1,22 @@ +[ + { + "name": "Inputs and Outputs", + "description": "", + "hidden": false, + "parameters": [ + "raw.data", + ] + }, + { + "name": "Other Parameters", + "description": "", + "hidden": false, + "parameters": [ + "core.binding.site.definition", + "DNA.sequence.column", + "affinity.column", + "header.present", + ] + } + +] diff --git a/build.xml b/build.xml index ff3322b..a212dde 100644 --- a/build.xml +++ b/build.xml @@ -1,5 +1,5 @@ - + diff --git a/manifest b/manifest index d85109c..81fcaf7 100644 --- a/manifest +++ b/manifest @@ -1,27 +1,28 @@ -#tfsites.defineTFBindingSites.from.PBM +# tfsites.NormalizeTfDnaAffinityData formerly tfsites.defineTFBindingSites.from.PBM #Mon Aug 21 20:23:30 UTC 2023 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-defineTfSitesPBM/01-defineTfSitesPBM.py -r -b -k -m -t -i -p -s -e +commandLine=python /build/tfsites-webportal/01-defineTfSites/01-defineTfSites.py -r -b -k -v -p +# -t 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.DefineTfSites/v1/ fileFormat= job.cpuCount= -job.docker.image=genepattern/tfsites\:0.10 +job.docker.image=genepattern/tfsites\:0.11 job.memory= job.walltime= language=any -name=tfsites.DefineTFBindingSites.from.PBM +name=tfsites.NormalizeTfDnaAffinityData os=any p1_MODE=IN p1_TYPE=FILE p1_default_value= -p1_description=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 affinity dataset. p1_fileFormat=.tsv p1_flag= -p1_name=raw.PBM.data +p1_name=raw.data p1_numValues=1..1 p1_optional= p1_prefix= @@ -32,10 +33,10 @@ p1_value= p2_MODE= p2_TYPE=TEXT p2_default_value=NNGGAWNN -p2_description=IUPAC definition of the core transcription factor binding site(see here). The length of the IUPAC definition should be the same length k as the k-mers in the raw PBM file. +p2_description=IUPAC definition of the core transcription factor binding site(see here). 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=binding.site.definition +p2_name=core.binding.site.definition p2_numValues=0..1 p2_optional= p2_prefix= @@ -46,10 +47,10 @@ p2_value= p3_MODE= p3_TYPE=Integer p3_default_value=1 -p3_description=Number of the column containing the forward DNA sequence in the raw PBM file (1-indexed, 1 is the first column). +p3_description=Number of the column containing the DNA sequences in the raw affinity file (1-indexed, 1 is the first column). p3_fileFormat= p3_flag= -p3_name=column.of.PBM.k-mers +p3_name=DNA.sequence.column p3_numValues=1..1 p3_optional= p3_prefix= @@ -57,103 +58,51 @@ p3_prefix_when_specified= p3_type=java.lang.Integer p3_value= + p4_MODE= p4_TYPE=Integer p4_default_value=4 -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_description=Number of the column containing the raw affinity values in the input file (1-indexed, 1 is the first column). p4_fileFormat= p4_flag= -p4_name=column.of.PBM.MFI -p4_numValues=0..1 +p4_name=affinity.column +p4_numValues=1..1 p4_optional= p4_prefix= p4_prefix_when_specified= p4_type=java.lang.Integer p4_value= + p5_MODE= p5_TYPE=TEXT -p5_default_value=.norm.pbm.tsv -p5_description=Name of the output file containing the normalized PBM data. -p5_fileFormat=tsv +p5_default_value=FALSE +p5_description=If True, a header exists in the PBM data file. If False, no header exists. +p5_fileFormat= p5_flag= -p5_name=reference.relative.affinity.table.output.filename +p5_name=header.present p5_numValues=0..1 p5_optional= p5_prefix= p5_prefix_when_specified= p5_type=java.lang.String -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, 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 -p7_numValues=0..1 -p7_optional= -p7_prefix= -p7_prefix_when_specified= -p7_type=java.lang.String -p7_value=FALSE\=FALSE;TRUE\=TRUE +p5_value=FALSE\=FALSE;TRUE\=TRUE -p8_MODE= -p8_TYPE=TEXT -p8_default_value=FALSE -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 -p8_numValues=0..1 -p8_optional= -p8_prefix= -p8_prefix_when_specified= -p8_type=java.lang.String -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 relative affinity values. -p9_fileFormat= -p9_flag= -p9_name=histograms.of.relative.affinity.output.filename -p9_numValues=0..1 -p9_optional= -p9_prefix= -p9_prefix_when_specified= -p9_type=java.lang.String -p9_value= +#p5_MODE= +#p5_TYPE=TEXT +#p5_default_value=.norm.pbm.tsv +#p5_description=Name of the output file containing the normalized PBM data. +#p5_fileFormat=tsv +#p5_flag= +#p5_name=reference.relative.affinity.table.output.filename +#p5_numValues=0..1 +#p5_optional= +#p5_prefix= +#p5_prefix_when_specified= +#p5_type=java.lang.String +#p5_value= -p10_MODE= -p10_TYPE=TEXT -p10_default_value= -p10_description=The k-mer sequence whose MFI will be used to normalize the MFI values of all other k-mers. The relative affinity for this k-mer will be 1.0. -p10_fileFormat= -p10_flag= -p10_name=define.highest.relative.affinity.sequence -p10_numValues=0..1 -p10_optional=on -p10_prefix= -p10_prefix_when_specified=-d -p10_type=java.lang.String -p10_value= privacy=public diff --git a/paramgroups.json b/paramgroups.json deleted file mode 100644 index 89d6221..0000000 --- a/paramgroups.json +++ /dev/null @@ -1,27 +0,0 @@ -[ - { - "name": "Inputs and Outputs", - "description": "", - "hidden": false, - "parameters": [ - "raw.PBM.data", - "reference.relative.affinity.table.output.filename", - "histograms.of.relative.affinity.output.filename" - ] - }, - { - "name": "Other Parameters", - "description": "", - "hidden": false, - "parameters": [ - "binding.site.definition", - "column.of.PBM.k-mers", - "column.of.PBM.MFI", - "header.present", - "report.sites.only", - "enforce.minimum.relative.affinity", - "define.highest.relative.affinity.sequence" - ] - } - -]