Mercurial > repos > iuc > vardict_java
changeset 3:e0734e88a104 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
| author | iuc |
|---|---|
| date | Thu, 27 Jan 2022 15:19:23 +0000 |
| parents | d262577e04b0 |
| children | |
| files | macros.xml split.py vardict.xml |
| diffstat | 3 files changed, 21 insertions(+), 2 deletions(-) [+] |
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--- a/macros.xml Tue Nov 16 19:05:56 2021 +0000 +++ b/macros.xml Thu Jan 27 15:19:23 2022 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@TOOL_VERSION@">1.8.3</token> <xml name="ref_select"> <conditional name="reference_source">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/split.py Thu Jan 27 15:19:23 2022 +0000 @@ -0,0 +1,16 @@ +import sys + + +fai = sys.argv[1] +chunk_size = int(sys.argv[2]) +overlap = int(sys.argv[3]) # Base pairs +with open(fai, 'r') as infile: + for line in infile: + name = line.split('\t')[0] + stop = int(line.split('\t')[1]) + start = 1 + while start < stop: + start = max(1, start - overlap) + print('\t'.join([name, str(start), + str(min(start + chunk_size, stop))])) + start += chunk_size
--- a/vardict.xml Tue Nov 16 19:05:56 2021 +0000 +++ b/vardict.xml Thu Jan 27 15:19:23 2022 +0000 @@ -4,6 +4,7 @@ <import>macros.xml</import> </macros> <requirements> + <requirement type="package" version="3.10.2">python</requirement> <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement> <requirement type="package" version="5.1.0">gawk</requirement> <requirement type="package" version="1.14">samtools</requirement> @@ -32,7 +33,7 @@ #else ln -s ./ref.fa.fai ./chromosomes.fa.fai && #end if - awk 'BEGIN {FS=OFS="\t"} {print $1, "1", $2}' ./chromosomes.fa.fai > ./regions.bed && + python '$__tool_directory__/split.py' ./chromosomes.fa.fai "\${VARDICT_CHUNKSIZE:-1000000}" "\${VARDICT_OVERLAP:-150}" > ./regions.bed && vardict-java #if $select_mode.mode == "paired" @@ -128,6 +129,7 @@ <param name="reference_source_selector" value="history"/> <param name="ref_file" ftype="fasta" value="genome.fasta" /> </conditional> + <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" /> <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" /> </test> @@ -141,6 +143,7 @@ <param name="reference_source_selector" value="cached"/> <param name="ref_file" value="test_buildid"/> </conditional> + <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" /> <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" /> </test>