Mercurial > repos > iuc > medaka_variant
changeset 7:28c13c42de01 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
| author | iuc |
|---|---|
| date | Mon, 22 Feb 2021 19:59:00 +0000 |
| parents | aabb4e1c0b7b |
| children | edf6d4003fad |
| files | convert_VCF_info_fields.py variant.xml |
| diffstat | 2 files changed, 27 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- 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=<ID=": id_ = line[11:].split(',')[0]
--- a/variant.xml Wed Feb 10 08:28:04 2021 +0000 +++ b/variant.xml Mon Feb 22 19:59:00 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@"> +<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@"> <description>Probability decoding</description> <macros> <import>macros.xml</import> @@ -9,6 +9,22 @@ </expand> <expand macro="version_command"/> + + <configfiles> + <configfile name="convert_fasta"> +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() + </configfile> + </configfiles> + <command detect_errors="exit_code"><![CDATA[ ## initialize @REF_FASTA@ @@ -48,9 +64,11 @@ #end if #if $out_annotated: + ## medaka annotate errors out if the reference is lower case at a position it's annotating because it checks vs the ref base in the vcf + && python '$convert_fasta' reference.fa upper_reference.fa && ln -s '$output_annotated.in_bam' in.bam && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai - && medaka tools annotate --pad $output_annotated.pad '$out_result' reference.fa in.bam tmp.vcf + && medaka tools annotate --pad $output_annotated.pad '$out_result' upper_reference.fa in.bam tmp.vcf && '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated' #end if ]]></command> @@ -167,8 +185,8 @@ <assert_contents> <has_n_lines n="22"/> <has_line line="##fileformat=VCFv4.1" /> - <has_line line="##medaka_version=1.0.3" /> <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" /> + <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" /> </assert_contents> </output> <output name="out_log">