WIP

manifest

@@ -2,8 +2,8 @@
 #Mon Aug 21 21:11:17 UTC 2023
 JVMLevel=
 LSID=urn:lsid:genepattern.org:module.analysis:00443
-author=
-commandLine=python /build/tfsites-webportal/04-annotateAndVisualizeInSilicoSnvs/04-annotateAndVisualizeInSilicoSnvs.py  <DNA.sequence(s).to.annotate> <PBM.or.PFM.reference.data.for.SNV.analysis>  <TF.information.for.plotting>  <all.TF.reference.data>  <SNV.effects.on.TF.sites.table.output.filename> <SNV.effects.on.TF.sites.annotated.image.output.filename>  <binding.site.definition.for.SNV.analysis> <reference.data.type.for.SNV.analysis>  <SNV.effects.to.report> <plot.denovo.sites> <optimization.threshold> <suboptimization.threshold> <plot.dimensions> <plot.resolution> <region.of.DNA.to.visualize> <number.of.bases.included.per.plot>
+author=Joe Salvasson, modified into a GenePattern module as Ted Liefeld
+commandLine=python /build/tfsites-webportal/04-annotateAndVisualizeInSilicoSnvs/04-annotateAndVisualizeInSilicoSnvs.py  <DNA.sequence(s).to.annotate> <PBM.or.PFM.reference.data.for.SNV.analysis>  <TF.information.for.plotting>  <all.TF.reference.data>   <TF.name.for.SNV.analysis>  <SNV.effects.to.report> <plot.denovo.sites> <optimization.threshold> <suboptimization.threshold> <output.image.format> <zoom.range> <window.size> <plot.dimensions> <plot.resolution>
 
 cpuType=any
 description=Creates a visualization showing all TF binding sites in a sequence.
@@ -33,7 +33,7 @@ p1_value=
 p2_MODE=IN
 p2_TYPE=FILE
 p2_default_value=
-p2_description=Normalized PBM data file for a transcription factor obtained from defineTFBindingSites.from.PBM or normalized PFM data file for a transcription factor from defineTFBindingSites.from.PFM. This is the transcription factor for which in-silico SNV analysis will be performed.
+p2_description=File containing the normalized PBM data obtained from defineTFBindingSites.from.PBM or normalized PFM data file from defineTFBindingSites.from.PFM. This is the transcription factor for which in silico SNV analysis will be performed.
 p2_fileFormat=.tsv
 p2_flag=
 p2_name=PBM.or.PFM.reference.data.for.SNV.analysis
@@ -75,177 +75,145 @@ p4_value=
 
 p5_MODE=
 p5_TYPE=TEXT
-p5_default_value=<DNA.sequence(s).to.annotate_basename>_snv_effects.tsv
-p5_description=Name of the output file containing the list of SNVs and their effects. Every possible mutation for each position in the sequence is labeled on the plot, and it is color-coded by the mutation type as indicated by the legend provided in the "TF information for plotting" file.
+p5_default_value=
+p5_description=Name of the transcription factor to use for SNV analysis.
 p5_fileFormat=
 p5_flag=
-p5_name=SNV.effects.on.TF.sites.table.output.filename
+p5_name=TF.name.for.SNV.analysis
 p5_numValues=0..1
 p5_optional=
 p5_prefix=
-p5_prefix_when_specified=-t  
+p5_prefix_when_specified=-s  
 p5_type=java.lang.String
 p5_value=
 
 p6_MODE=
 p6_TYPE=TEXT
-p6_default_value=<DNA.sequence(s).to.annotate_basename>_snv_effects.png
-p6_description=Base name of the output file for the plots. If the length of the sequence is greater than 500, the visualization will be broken up into multiple output files with the following name format: [base name]_zoom=[start pos],[end pos].png
+p6_default_value=Window
+p6_description=Select the format in which the images will be outputted. Zoom indicates the region of the DNA sequence to visualize, given a start and end coordinate, which can be specified using the zoom range option below. Windows will output the entire DNA sequence into separate images. The size of the window, or the number of bases plotted per window, can be specified by the window size option below.
 p6_fileFormat=
 p6_flag=
-p6_name=SNV.effects.on.TF.sites.annotated.image.output.filename
-p6_numValues=0..1
+p6_name=output.image.format
+p6_numValues=1..1
 p6_optional=
 p6_prefix=
-p6_prefix_when_specified=-i  
+p6_prefix_when_specified=-r  
 p6_type=java.lang.String
-p6_value=
-
-
+p6_value=Window;Zoom
 
 p7_MODE=
 p7_TYPE=TEXT
-p7_default_value=NNGGAWNN
-p7_description=IUPAC definition of the core binding site to conduct SNV analysis (see <a href="https://www.bioinformatics.org/sms/iupac.html">here</a>).
+p7_default_value=all
+p7_description=Specify one or more mutation types to analyze. SNV mutations can either increase (optimize) or decrease (sub-optimize) the affinity/score, delete a binding site, or create a binding site. Therefore, the possible mutation types are 'inc', 'dec', 'denovo', and 'del.' This option also takes the value 'all' if the user would like to analyze all of the listed mutation types.
 p7_fileFormat=
 p7_flag=
-p7_name=binding.site.definition.for.SNV.analysis
-p7_numValues=0..1
-p7_optional=
+p7_name=SNV.effects.to.report
+p7_numValues=1..1
+p7_optional=on
 p7_prefix=
-p7_prefix_when_specified=-s  
+p7_prefix_when_specified=-e 
 p7_type=java.lang.String
 p7_value=
 
-
 p8_MODE=
 p8_TYPE=TEXT
-p8_default_value=PBM
-p8_description=Specify whether PBM or PFM reference is being used to annotate binding sites.
+p8_default_value=TRUE
+p8_description=f True, plot binding sites that would be created from denovo SNVs, in addition to existing binding sites. If False, only plot existing binding sites.
 p8_fileFormat=
 p8_flag=
-p8_name=reference.data.type.for.SNV.analysis
+p8_name=plot.denovo.sites
 p8_numValues=1..1
 p8_optional=
 p8_prefix=
-p8_prefix_when_specified=-r  
+p8_prefix_when_specified=-n  
 p8_type=java.lang.String
-p8_value=PBM=PBM;PFM=PFM
+p8_value=TRUE=TRUE;FALSE=FALSE
 
 
 p9_MODE=
 p9_TYPE=TEXT
-p9_default_value=all
-p9_description=Specify one or more mutation types to analyze. SNV mutations can either increase (optimize) or decrease (sub-optimize) the affinity, delete a binding site, or create a binding site. Therefore, the possible mutation types are 'inc', 'dec', 'denovo', and 'del.' This option also takes the value 'all' if the user would like to analyze all of the listed mutation types.
+p9_default_value=1.0
+p9_description=Fold change threshold for mutations that increase the affinity/score. Only SNVs with fold change above this threshold will be reported. By default, all SNVs will be reported.
 p9_fileFormat=
 p9_flag=
-p9_name=SNV.effects.to.report
-p9_numValues=1..1
-p9_optional=on
+p9_name=optimization.threshold
+p9_numValues=0..1
+p9_optional=
 p9_prefix=
-p9_prefix_when_specified=-e 
+p9_prefix_when_specified=-o  
 p9_type=java.lang.String
 p9_value=
 
 p10_MODE=
 p10_TYPE=TEXT
-p10_default_value=TRUE
-p10_description=f True, plot binding sites that would be created from denovo SNVs, in addition to existing binding sites. If False, only plot existing binding sites.
+p10_default_value=1.0
+p10_description=Fold change threshold for mutations that decrease the affinity/score. Only SNVs with fold change below this threshold will be reported. By default, all SNVs will be reported.
 p10_fileFormat=
 p10_flag=
-p10_name=plot.denovo.sites
-p10_numValues=1..1
+p10_name=suboptimization.threshold
+p10_numValues=0..1
 p10_optional=
 p10_prefix=
-p10_prefix_when_specified=-n  
+p10_prefix_when_specified=-z  
 p10_type=java.lang.String
-p10_value=TRUE=TRUE;FALSE=FALSE
-
+p10_value=
 
 p11_MODE=
 p11_TYPE=TEXT
-p11_default_value=1.5
-p11_description=Fold-change threshold for affinity-increasing mutations. Only SNVs with fold change above this threshold will be reported. By default, all will be reported.
+p11_default_value=
+p11_description=Height and width of the image in inches.
 p11_fileFormat=
 p11_flag=
-p11_name=optimization.threshold
+p11_name=plot.dimensions
 p11_numValues=0..1
-p11_optional=
+p11_optional=on
 p11_prefix=
-p11_prefix_when_specified=-o  
+p11_prefix_when_specified=-m  
 p11_type=java.lang.String
 p11_value=
 
 p12_MODE=
 p12_TYPE=TEXT
-p12_default_value=0.9
-p12_description=Fold-change threshold for affinity-decreasing mutations. Only SNVs with fold change below this threshold will be reported. By default, all will be reported.
+p12_default_value=200
+p12_description=Resolution of the plot, in dots (pixels) per inch.
 p12_fileFormat=
 p12_flag=
-p12_name=suboptimization.threshold
+p12_name=plot.resolution
 p12_numValues=0..1
 p12_optional=
 p12_prefix=
-p12_prefix_when_specified=-z  
+p12_prefix_when_specified=-l  
 p12_type=java.lang.String
 p12_value=
 
 p13_MODE=
 p13_TYPE=TEXT
 p13_default_value=
-p13_description=Height and width of the image in inches.
+p13_description=Given a start position and an end position, zoom into a portion of the sequence. The numbers in the range are inclusive and 0-indexed. For example, the first 200 nucleotides of the sequence would be specified as: 0-199.
 p13_fileFormat=
 p13_flag=
-p13_name=plot.dimensions
+p13_name=zoom.range
 p13_numValues=0..1
 p13_optional=on
 p13_prefix=
-p13_prefix_when_specified=-m  
+p13_prefix_when_specified=-v  
 p13_type=java.lang.String
 p13_value=
 
 p14_MODE=
 p14_TYPE=TEXT
-p14_default_value=200
-p14_description=Resolution of the plot, in dots (pixels) per inch.
+p14_default_value=500
+p14_description=Interval size (in nucleotides) to separate the output plot into. By default, the sequence will be divided into 500-nucleotide segments.
 p14_fileFormat=
 p14_flag=
-p14_name=plot.resolution
+p14_name=window.size
 p14_numValues=0..1
-p14_optional=
+p14_optional=on
 p14_prefix=
-p14_prefix_when_specified=-l  
+p14_prefix_when_specified=-f  
 p14_type=java.lang.String
 p14_value=
 
-p15_MODE=
-p15_TYPE=TEXT
-p15_default_value=
-p15_description=Given a start position and an end position, zoom into a portion of the sequence. The numbers in the range are inclusive. For example, the first 200 nucleotides of the sequence would be specified as: 1-200.
-p15_fileFormat=
-p15_flag=
-p15_name=region.of.DNA.to.visualize
-p15_numValues=0..1
-p15_optional=on
-p15_prefix=
-p15_prefix_when_specified=-v  
-p15_type=java.lang.String
-p15_value=
-
-p16_MODE=
-p16_TYPE=TEXT
-p16_default_value=500
-p16_description=Interval size (in nucleotides) to separate the output plot into. By default, the sequence will be divided into 500-nucleotide segments.
-p16_fileFormat=
-p16_flag=
-p16_name=number.of.bases.included.per.plot
-p16_numValues=0..1
-p16_optional=on
-p16_prefix=
-p16_prefix_when_specified=-f  
-p16_type=java.lang.String
-p16_value=
-
 privacy=public
 quality=development
 src.repo=

paramgroups.json

@@ -8,18 +8,16 @@
             "PBM.or.PFM.reference.data.for.SNV.analysis",
             "TF.information.for.plotting",
             "all.TF.reference.data",
-            "SNV.effects.on.TF.sites.table.output.filename",
-            "SNV.effects.on.TF.sites.annotated.image.output.filename"
         ]
     },
     {
-        "name": "Analysis Parameters",
+        "name": "Other Parameters",
         "description": "",
         "hidden": false,
         "parameters": [
-            "binding.site.definition.for.SNV.analysis",
-	    "reference.data.type.for.SNV.analysis",
+            "TF.name.for.SNV.analysis",
             "SNV.effects.to.report",
+            "plot.denovo.sites",
             "optimization.threshold",
             "suboptimization.threshold"
         ]
@@ -29,11 +27,11 @@
         "description": "",
         "hidden": false,
         "parameters": [
-            "plot.denovo.sites",
+            "output.image.format",
+            "zoom.range",
+            "window.size",
             "plot.dimensions",
             "plot.resolution",
-            "region.of.DNA.to.visualize",
-            "number.of.bases.included.per.plot"
         ]
     }
 ]