Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.4+galaxy2 |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.3.1+galaxy2 |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.3.1+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.3.1+galaxy0 |
lofreq_call |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
lofreq | 2.1.5 | package |
Additional information about this tool |
## prepare reference genome and mapped reads input #if str($reference_source.ref_selector) == 'history': #set $reference_fasta_fn = 'reference.fa' ln -s '$reference_source.ref' $reference_fasta_fn && lofreq faidx $reference_fasta_fn 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && #else #set $reference_fasta_fn = str($reference_source.ref.fields.path) #end if ln -s '$reads' reads.bam && ln -s -f '${reads.metadata.bam_index}' reads.bam.bai && #if str($call_control.set_call_options) == 'yes': #set $ign_vcfs = [] #if str($call_control.source_qual.use_src_qual.src_qual): #for $n, $ign_vcf in enumerate($call_control.source_qual.use_src_qual.ign_vcf): ## lofreq recognizes compressed vcf input based on its .gz ## suffix => symlink all datasets with standard extensions. ## For bgzipped vcfs, also make the index files available. #if $ign_vcf: #if $ign_vcf.is_of_type('vcf_bgzip'): #set $ign_src = 'ign%d.vcf.gz' % $n ln -s '$ign_vcf' $ign_src && ln -s '$ign_vcf.metadata.tabix_index' ${ign_src}.tbi && #else: #set $ign_src = 'ign%d.vcf' % $n ln -s '$ign_vcf' $ign_src && #end if #silent $ign_vcfs.append($ign_src) #end if #end for #end if #set $ign_vcfs = ','.join($ign_vcfs) #end if ## call variants with lofreq lofreq call-parallel --pp-threads \${GALAXY_SLOTS:-1} --verbose --ref '$reference_fasta_fn' --out variants.vcf $variant_types #if str($regions.restrict_to_region) == 'regions_from_file': --bed '$regions.bed' #end if #if str($call_control.set_call_options) == 'yes': --min-cov $call_control.coverage.min_cov --max-depth $call_control.coverage.max_depth $call_control.pe.use_orphan --min-bq $call_control.bc_quals.min_bq #if $call_control.bc_quals.min_alt_bq > $call_control.bc_quals.min_bq: --min-alt-bq $call_control.bc_quals.min_alt_bq #else: --min-alt-bq $call_control.bc_quals.min_bq #end if #if str($call_control.bc_quals.alt_bq.modify): --def-alt-bq $call_control.bc_quals.alt_bq.def_alt_bq #end if ${call_control.align_quals.alnqual.use_alnqual} #if str($call_control.align_quals.alnqual.use_alnqual) != '-A -B': ${call_control.align_quals.alnqual.alnqual_choice.alnquals_to_use} ${call_control.align_quals.alnqual.alnqual_choice.extended_baq} #end if --min-mq $call_control.map_quals.min_mq #if str($call_control.map_quals.use_mq.no_mq): $call_control.map_quals.use_mq.no_mq #else: #if $call_control.map_quals.use_mq.max_mq > $call_control.map_quals.min_mq: --max-mq $call_control.map_quals.use_mq.max_mq #else: --max-mq $call_control.map_quals.min_mq #end if #end if #if str($call_control.source_qual.use_src_qual.src_qual): $call_control.source_qual.use_src_qual.src_qual #if $ign_vcfs: --ign-vcf '$ign_vcfs' #end if --def-nm-q $call_control.source_qual.use_src_qual.def_nm_q #end if --min-jq $call_control.joint_qual.min_jq --min-alt-jq $call_control.joint_qual.min_alt_jq --def-alt-jq $call_control.joint_qual.def_alt_jq #end if --sig $filter_control.sig #set $bonf_factor = $filter_control.bonf or 'dynamic' --bonf $bonf_factor $filter_control.others reads.bam 2>&1 ## in case of errors add the log files produced ## by the parallel workers to stderr || (tool_exit_code=\$? && cat "\$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit \$tool_exit_code) ## work around a bug in lofreq call-parallel ## https://github.com/CSB5/lofreq/issues/85 ## that causes the output format to be vcf.gz with certain filter ## combinations. Issue is closed but still not fixed. #if str($bonf_factor) != 'dynamic': #if '--no-default-filter' in str($filter_control.others): && ln -s variants.vcf variants.vcf.gz && gzip -df variants.vcf.gz #end if #end if && echo $filter_control.filter_type
Functional tests |
name | inputs | outputs | required files |
Test-1 |
reads: lofreq-in1.bam reference_source|ref: pBR322.fa reference_source|ref_selector: history |
name: value |
lofreq-in1.bam pBR322.fa value |
Test-2 |
reads: lofreq-in1.bam reference_source|ref: pBR322.fa reference_source|ref_selector: history call_control|set_call_options: yes |
name: value |
lofreq-in1.bam pBR322.fa value |
Test-3 |
reads: lofreq-in1.bam reference_source|ref: pBR322.fa reference_source|ref_selector: history call_control|source_qual|use_src_qual|def_nm_q: 40 call_control|source_qual|use_src_qual|ign_vcf: call-out1.vcf call_control|source_qual|use_src_qual|src_qual: --src-qual call_control|set_call_options: yes |
name: value |
lofreq-in1.bam pBR322.fa call-out1.vcf value |
Test-4 |
reads: lofreq-in1.bam reference_source|ref: pBR322.fa reference_source|ref_selector: history filter_control|filter_type: set_all_off |
name: value |
lofreq-in1.bam pBR322.fa value |
Test-5 |
reads: indelqual-out3.bam reference_source|ref: pBR322.fa reference_source|ref_selector: history variant_types: --call-indels --only-indels filter_control|filter_type: set_all_off |
name: value |
indelqual-out3.bam pBR322.fa value |