From 6ad0c7fda1cfba9fce3d4dabece81b01b16c799d Mon Sep 17 00:00:00 2001 From: liefeld Date: Tue, 26 Nov 2024 08:44:00 -0800 Subject: [PATCH] Round 2 ov Nov updates, 2 new parameters added and flags for others changed for no good reason --- _paramgroups.json | 22 -------------- manifest | 73 +++++++++++++++++++++++++++++++++-------------- 2 files changed, 52 insertions(+), 43 deletions(-) delete mode 100644 _paramgroups.json diff --git a/_paramgroups.json b/_paramgroups.json deleted file mode 100644 index c3dd286..0000000 --- a/_paramgroups.json +++ /dev/null @@ -1,22 +0,0 @@ -[ - { - "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/manifest b/manifest index 6f9e803..72db4c1 100644 --- a/manifest +++ b/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 -b -k -v -p +commandLine=python /build/tfsites-webportal/01-normalizeTfDnaAffinityData/01-normalizeTfDnaAffinityData.py -r -b -d -a -p -S -o # -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.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 @@ -30,13 +30,14 @@ 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_ 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=core.binding.site.definition +p2_name=output.filename.prefix p2_numValues=0..1 p2_optional= p2_prefix= @@ -44,28 +45,28 @@ 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 here). 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=