--- a/CompareSTR/compareSTR.xml	Sat Apr 23 16:34:03 2022 +0000
+++ b/CompareSTR/compareSTR.xml	Sun May 15 15:23:59 2022 +0000
@@ -1,4 +1,3 @@
-<?xml version="1.0" ?>
 <tool id="compareSTR" name="CompareSTR" version="@tool_version@">
     <description>CompareSTR compares different TR callsets generated on the same samples against the same reference
         panel. CompareSTR outputs overall, per-locus, and per-sample concordance information.
@@ -183,18 +182,18 @@
 
     <tests>
         <test>
-            <section name="required">
-                <param name="vcf1" value="NA12878_chr21_hipstr.sorted.vcf.gz"/>
-                <param name="vcf2" value="NA12878_chr21_hipstr.sorted.vcf.gz"/>
+            <section name="required_arguments">
+                <param name="vcf1" value="NA12878_chr21_hipstr.sorted.vcf.gz" />
+                <param name="vcf2" value="NA12878_chr21_hipstr.sorted.vcf.gz" />
                 <param name="out" value="test_result"/>
             </section>
 
-            <section name="stratification">
+            <section name="metrics_to_stratify_results">
                 <param name="stratify_fields" value="DP,Q"/>
                 <param name="stratify_binsizes" value="0:50:5,0:1:0.1"/>
                 <param name="stratify_file" value="0"/>
             </section>
-            <section name="other">
+            <section name="optional_arguments">
                 <param name="verbose" value="true"/>
                 <param name="vcftype1" value="hipstr"/>
                 <param name="vcftype2" value="hipstr"/>
@@ -230,50 +229,52 @@
     </tests>
 
 
-    <help>usage: main.py [-h] --vcf1 VCF1 --vcf2 VCF2 --out OUT [--samples SAMPLES] [--region REGION] [--stratify-fields
-        STRATIFY_FIELDS] [--stratify-binsizes STRATIFY_BINSIZES] [--stratify-file STRATIFY_FILE] [--period]
-        [--bubble-min BUBBLE_MIN] [--bubble-max BUBBLE_MAX] [--verbose] [--numrecords NUMRECORDS] [--noplot] [--vcftype1
-        VCFTYPE1] [--vcftype2 VCFTYPE2] [--ignore-phasing] [--version]
+    <help>usage: pygalgen [-h] --vcf1 VCF1 --vcf2 VCF2 --out OUT [--samples SAMPLES] [--region REGION]
+                [--stratify-fields STRATIFY_FIELDS] [--stratify-binsizes STRATIFY_BINSIZES]
+                [--stratify-file STRATIFY_FILE] [--period] [--bubble-min BUBBLE_MIN] [--bubble-max BUBBLE_MAX]
+                [--verbose] [--numrecords NUMRECORDS] [--noplot] [--vcftype1 VCFTYPE1] [--vcftype2 VCFTYPE2]
+                [--ignore-phasing] [--version]
 
-        options:
-        -h, --help show this help message and exit
+options:
+  -h, --help            show this help message and exit
 
-        Required arguments:
-        --vcf1 VCF1 First VCF file to compare (must be sorted, bgzipped, and indexed)
-        --vcf2 VCF2 Second VCF file to compare (must be sorted, bgzipped, and indexed)
-        --out OUT Prefix to name output files
+Required arguments:
+  --vcf1 VCF1           First VCF file to compare (must be sorted, bgzipped, and indexed)
+  --vcf2 VCF2           Second VCF file to compare (must be sorted, bgzipped, and indexed)
+  --out OUT             Prefix to name output files
 
-        Filtering options:
-        --samples SAMPLES File containing list of samples to include
-        --region REGION Restrict to this region chrom:start-end
+Filtering options:
+  --samples SAMPLES     File containing list of samples to include
+  --region REGION       Restrict to this region chrom:start-end
 
-        Metrics to stratify results:
-        --stratify-fields STRATIFY_FIELDS
-        Comma-separated list of FORMAT fields to stratify by
-        --stratify-binsizes STRATIFY_BINSIZES
-        Comma-separated list of min:max:binsize to stratify each field on. Must be same length as --stratify-fields.
-        --stratify-file STRATIFY_FILE
-        Set to 1 to stratify based on --vcf1. Set to 2 to stratify based on --vcf2. Set to 0 to apply stratification to
-        both --vcf1 and --vcf2
-        --period Report results overall and also stratified by repeat unit length (period)
+Metrics to stratify results:
+  --stratify-fields STRATIFY_FIELDS
+                        Comma-separated list of FORMAT fields to stratify by
+  --stratify-binsizes STRATIFY_BINSIZES
+                        Comma-separated list of min:max:binsize to stratify each field on. Must be same length as
+                        --stratify-fields.
+  --stratify-file STRATIFY_FILE
+                        Set to 1 to stratify based on --vcf1. Set to 2 to stratify based on --vcf2. Set to 0 to apply
+                        stratification to both --vcf1 and --vcf2
+  --period              Report results overall and also stratified by repeat unit length (period)
 
-        Plotting options:
-        --bubble-min BUBBLE_MIN
-        Minimum x/y axis value to display on bubble plots
-        --bubble-max BUBBLE_MAX
-        Maximum x/y axis value to display on bubble plots
+Plotting options:
+  --bubble-min BUBBLE_MIN
+                        Minimum x/y axis value to display on bubble plots
+  --bubble-max BUBBLE_MAX
+                        Maximum x/y axis value to display on bubble plots
 
-        Optional arguments:
-        --verbose Print helpful debugging info
-        --numrecords NUMRECORDS
-        For debugging, only process this many records
-        --noplot Don't output any plots. Only produce text output
-        --vcftype1 VCFTYPE1 ##!!## Name trh could not be loaded
-        --vcftype2 VCFTYPE2 ##!!## Name trh could not be loaded
-        --ignore-phasing Treat all calls as if they are unphased
+Optional arguments:
+  --verbose             Print helpful debugging info
+  --numrecords NUMRECORDS
+                        For debugging, only process this many records
+  --noplot              Don't output any plots. Only produce text output
+  --vcftype1 VCFTYPE1   Name of genotyper that created the first vcf
+  --vcftype2 VCFTYPE2   Name of genotyper that created the second vcf
+  --ignore-phasing      Treat all calls as if they are unphased
 
-        Version:
-        --version show program's version number and exit
+Version:
+  --version             show program's version number and exit
     </help>