Repository 'medaka_variant'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant

Changeset 7:28c13c42de01 (2021-02-22)
 Previous changeset 6:aabb4e1c0b7b (2021-02-10) Next changeset 8:edf6d4003fad (2021-02-23) Commit message: "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a" modified: convert_VCF_info_fields.py variant.xml b diff -r aabb4e1c0b7b -r 28c13c42de01 convert_VCF_info_fields.py--- a/convert_VCF_info_fields.py Wed Feb 10 08:28:04 2021 +0000+++ b/convert_VCF_info_fields.py Mon Feb 22 19:59:00 2021 +0000 [ @@ -15,7 +15,11 @@   def pval_to_phredqual(pval):-    return round(-10 * log10(pval))+    try:+        ret = round(-10 * log10(pval))+    except ValueError:+        ret = 2147483647  # transform pval of 0.0 to max signed 32 bit int+    return ret   def parseInfoField(info):@@ -33,7 +37,7 @@     to_skip = set(['SC', 'SR'])     for i, line in enumerate(in_vcf):         if i == 1:-            out_vcf.write("##convert_VCF_info_fields=0.1\n")+            out_vcf.write("##convert_VCF_info_fields=0.2\n")         if line[0:2] == "##":             if line[0:11] == "##INFO=-+     Probability decoding              macros.xml@@ -9,6 +9,22 @@           ++    +        +import sys+infile = open(sys.argv[1], 'r')+outfile = open(sys.argv[2], 'w')+for line in infile:+    if line[0] == '>':+        outfile.write(line)+    else:+        outfile.write(line.upper())+infile.close()+outfile.close()+        +    +     @@ -167,8 +185,8 @@                                                           -                                         +