Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/vardict_java/vardict_java/1.8.3+galaxy1 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/vardict_java/vardict_java/1.8.3+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/vardict_java/vardict_java/1.8.1+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/vardict_java/vardict_java/1.7.0+galaxy0 |
vardict_java |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
python | 3.10.2 | package |
vardict-java | 1.8.3 | package |
gawk | 5.1.0 | package |
samtools | 1.14 | package |
Additional information about this tool |
#if $select_mode.mode == "paired" ln -s '$select_mode.normal' ./normal.bam && ln -s '$select_mode.normal.metadata.bam_index' ./normal.bam.bai && #end if ln -s '$select_mode.tumor' ./tumor.bam && ln -s '$select_mode.tumor.metadata.bam_index' ./tumor.bam.bai && ## INDEX REFERENCE FASTA FILE IF FROM HISTORY #if $reference_source.reference_source_selector == "history": ln -s '$reference_source.ref_file' ./ref.fa && samtools faidx ./ref.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for vardict' >&2 && #else if $reference_source.reference_source_selector == "cached" ln -s '$reference_source.ref_file.fields.path' ./ref.fa && ln -s '${reference_source.ref_file.fields.path}.fai' ./ref.fa.fai && #end if ## build BED file from chromosome list #if $interval_file: grep -w -f '$interval_file' ./ref.fa.fai > ./chromosomes.fa.fai && #else ln -s ./ref.fa.fai ./chromosomes.fa.fai && #end if python '$__tool_directory__/split.py' ./chromosomes.fa.fai "\${VARDICT_CHUNKSIZE:-1000000}" "\${VARDICT_OVERLAP:-150}" > ./regions.bed && vardict-java #if $select_mode.mode == "paired" -b "./tumor.bam|./normal.bam" -N 'Tumor' #else -b "./tumor.bam" -N 'Sample' #end if -G ./ref.fa -z -th \${GALAXY_SLOTS:-1} -f '$advancedsettings.f' -k '$advancedsettings.k' -r '$advancedsettings.r' -B '$advancedsettings.B' -Q '$advancedsettings.Q' -q '$advancedsettings.q' -m '$advancedsettings.m' -T '$advancedsettings.T' -X '$advancedsettings.X' -P '$advancedsettings.P' -o '$advancedsettings.o' -O '$advancedsettings.O' -V '$advancedsettings.V' ## construct VFC table -c 1 -S 2 -E 3 -g 4 ./regions.bed ## postprocessing #if $select_mode.mode == "paired" | testsomatic.R | var2vcf_paired.pl -N 'Tumor|Normal' #else | teststrandbias.R | var2vcf_valid.pl -N 'Sample' -E #end if -f '$advancedsettings.f' > '$all_variants' && ## Filter for PASS variants awk 'BEGIN {FS=OFS="\t"} substr(\$0, 1, 1) == "#" {print \$0; next} \$7 == "PASS" {print \$0}' '$all_variants' > '$passed_variants'
Functional tests |
name | inputs | outputs | required files |
Test-1 |
select_mode|normal: normal.bam select_mode|tumor: tumor.bam select_mode|mode: paired reference_source|ref_file: genome.fasta reference_source|reference_source_selector: history |
name: value name: value |
normal.bam tumor.bam genome.fasta value |
Test-2 |
select_mode|normal: normal.bam select_mode|tumor: tumor.bam select_mode|mode: paired reference_source|ref_file: test_buildid reference_source|reference_source_selector: cached |
name: value name: value |
normal.bam tumor.bam value |
Test-3 |
select_mode|tumor: tumor.bam select_mode|mode: single reference_source|ref_file: test_buildid reference_source|reference_source_selector: cached |
name: value name: value |
tumor.bam value |