From 6480674da588d5d654faf4f6a62d3bba63252df6 Mon Sep 17 00:00:00 2001
From: ted Liefeld <liefeld@broadinstitute.org>
Date: Wed, 14 Feb 2024 16:14:46 -0800
Subject: [PATCH] Updated descriptions and parameter names to match new doc

---
 build.xml |  2 +-
 manifest  | 24 ++++++++++++------------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/build.xml b/build.xml
index 1d77d1e..1bebd9e 100644
--- a/build.xml
+++ b/build.xml
@@ -6,7 +6,7 @@
 <target name="create-zip" depends="init">
     <antcall target="prezip"/>
     <zip destfile="${dest.dir}/${ant.project.name}.zip" whenempty="fail" defaultexcludes="true">
-        <fileset dir="." includes="manifest, Dockerfile, LICENSE"/>
+        <fileset dir="." includes="manifest, Dockerfile, LICENSE, paramgroups.json"/>
         <!-- zipfileset dir="src" includes="*.py"/-->
     </zip>
     <antcall target="postzip"/>
diff --git a/manifest b/manifest
index 231c9cc..82f65d1 100644
--- a/manifest
+++ b/manifest
@@ -3,13 +3,13 @@
 JVMLevel=
 LSID=
 author=
-commandLine=python /build/tfsites-webportal/05-integrateGenomeAnnotations/05-integrateGenomeAnnotations.GENEPATTERN.py -f <input.data> -o <out.filename> -z <zero.pos> <bed.file>       
+commandLine=python /build/tfsites-webportal/05-integrateGenomeAnnotations/05-integrateGenomeAnnotations.GENEPATTERN.py -f <genotypic.data.input> -o <genotypic.&.BED.overlap.filename> -z <zero.index.genomic.coordinates> <bed.genomic.interval.data>       
 cpuType=any
-description=tfsites.IntegrateGenomeAnnotations finds all possible SNVs and their effects on binding sites.
+description=Checks whether overlap exists between a list of mutations in a genotypic dataset and BED files containing genomic regions of interest. For each mutation, it is reported whether or not the region of each mutation overlaps with the regions contained within each BED file.
 documentationUrl=https://genepattern.github.io/tfsites.IntegrateGenomeAnnotations/v1/
 fileFormat=
 job.cpuCount=
-job.docker.image=genepattern/tfsites\:0.4
+job.docker.image=genepattern/tfsites\:0.6
 job.memory=
 job.walltime=
 language=any
@@ -18,10 +18,10 @@ os=any
 p1_MODE=IN
 p1_TYPE=FILE
 p1_default_value=
-p1_description=File containing a list of SNVs.
+p1_description=A .tsv file containing a list of mutations from a genotypic experiment, along with their genomic position. It can also contain columns with other information, such as the statistical association between the mutation and a phenotype. 
 p1_fileFormat=.tsv
 p1_flag=
-p1_name=input.data
+p1_name=genotypic.data.input
 p1_numValues=1..1
 p1_optional=
 p1_prefix=
@@ -32,10 +32,10 @@ p1_value=
 p2_MODE=
 p2_TYPE=TEXT
 p2_default_value=TRUE
-p2_description=TRUE/FALSE, genomic coordinates are 0-indexed.
+p2_description=If True, the genomic coordinates in the input eQTL file are 0-indexed (sequence numbering starts at 0). If False, they are 1-indexed (sequence numbering starts at 1).
 p2_fileFormat=
 p2_flag=
-p2_name=zero.pos
+p2_name=zero.index.genomic.coordinates
 p2_numValues=1..1
 p2_optional=
 p2_prefix=
@@ -45,11 +45,11 @@ p2_value=FALSE\=FALSE;TRUE\=TRUE
 
 p3_MODE=
 p3_TYPE=TEXT
-p3_default_value=<input.data_basename>_overlap.tsv
-p3_description=Out file name for the list of SNVs and their effects
+p3_default_value=<genotypic.data.input_basename>_overlap.tsv
+p3_description=Output file name for the annotated PBM data.
 p3_fileFormat=
 p3_flag=
-p3_name=out.filename
+p3_name=genotypic.&.BED.overlap.filename
 p3_numValues=0..1
 p3_optional=
 p3_prefix=
@@ -60,10 +60,10 @@ p3_value=
 p4_MODE=IN
 p4_TYPE=FILE
 p4_default_value=
-p4_description=Bed files to overlap with genomic coordinates in input file.
+p4_description=A BED file containing a list of genomic intervals of interest.
 p4_fileFormat=.bed
 p4_flag=
-p4_name=bed.file
+p4_name=bed.genomic.interval.data
 p4_numValues=1..11
 p4_optional=on
 p4_prefix=