lofreq_call: lofreq_call.xml annotate

annotate lofreq_call.xml @ 5:65432c3abf6c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"

author	iuc
date	Mon, 15 Jun 2020 13:13:03 -0400
parents	3b4b2121842f
children	e1461b5c52a0

rev	line source
5 65432c3abf6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528" iuc parents: 3 diff changeset	1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy0">
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	2 <description>with LoFreq</description>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	3 <macros>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	4 <import>macros.xml</import>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	5 </macros>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	6 <expand macro="requirements" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	7 <command detect_errors="exit_code"><![CDATA[
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	8 ## prepare reference genome and mapped reads input
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	9 @PREPARE_REF@
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	10 ln -s '$reads' reads.bam &&
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	11 ln -s -f '${reads.metadata.bam_index}' reads.bam.bai &&
2 dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	12 #if str($call_control.set_call_options) == 'yes':
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	13 #set $ign_vcfs = []
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	14 #if str($call_control.source_qual.use_src_qual.src_qual):
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	15 #for $n, $ign_vcf in enumerate($call_control.source_qual.use_src_qual.ign_vcf):
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	16 ## lofreq recognizes compressed vcf input based on its .gz
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	17 ## suffix => symlink all datasets with standard extensions.
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	18 ## For bgzipped vcfs, also make the index files available.
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	19 #if $ign_vcf:
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	20 #if $ign_vcf.is_of_type('vcf_bgzip'):
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	21 #set $ign_src = 'ign%d.vcf.gz' % $n
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	22 ln -s '$ign_vcf' $ign_src &&
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	23 ln -s '$ign_vcf.metadata.tabix_index' ${ign_src}.tbi &&
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	24 #else:
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	25 #set $ign_src = 'ign%d.vcf' % $n
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	26 ln -s '$ign_vcf' $ign_src &&
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	27 #end if
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	28 #silent $ign_vcfs.append($ign_src)
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	29 #end if
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	30 #end for
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	31 #end if
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	32 #set $ign_vcfs = ','.join($ign_vcfs)
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	33 #end if
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	34
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	35 ## call variants with lofreq
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	36
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	37 ## make lofreq stick to tool contract by
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	38 ## generating tmp output inside job working dir
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	39 mkdir pp-tmp &&
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	40 export TMPDIR=pp-tmp &&
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	41
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	42 lofreq call-parallel --pp-threads \${GALAXY_SLOTS:-1} --verbose
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	43
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	44 --ref '$reference_fasta_fn' --out variants.vcf $variant_types
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	45
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	46 #if str($regions.restrict_to_region) == 'regions_from_file':
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	47 --bed '$regions.bed'
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	48 #end if
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	49
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	50 #if str($call_control.set_call_options) == 'yes':
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	51 --min-cov $call_control.coverage.min_cov
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	52 --max-depth $call_control.coverage.max_depth
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	53 $call_control.pe.use_orphan
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	54 --min-bq $call_control.bc_quals.min_bq
2 dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	55 #if $call_control.bc_quals.min_alt_bq > $call_control.bc_quals.min_bq:
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	56 --min-alt-bq $call_control.bc_quals.min_alt_bq
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	57 #else:
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	58 --min-alt-bq $call_control.bc_quals.min_bq
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	59 #end if
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	60 #if str($call_control.bc_quals.alt_bq.modify):
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	61 --def-alt-bq $call_control.bc_quals.alt_bq.def_alt_bq
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	62 #end if
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	63 ${call_control.align_quals.alnqual.use_alnqual}
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	64 #if str($call_control.align_quals.alnqual.use_alnqual) != '-A -B':
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	65 ${call_control.align_quals.alnqual.alnqual_choice.alnquals_to_use}
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	66 ${call_control.align_quals.alnqual.alnqual_choice.extended_baq}
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	67 #end if
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	68 --min-mq $call_control.map_quals.min_mq
2 dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	69 #if str($call_control.map_quals.use_mq.no_mq):
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	70 $call_control.map_quals.use_mq.no_mq
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	71 #else:
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	72 #if $call_control.map_quals.use_mq.max_mq > $call_control.map_quals.min_mq:
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	73 --max-mq $call_control.map_quals.use_mq.max_mq
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	74 #else:
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	75 --max-mq $call_control.map_quals.min_mq
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	76 #end if
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	77 #end if
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	78 #if str($call_control.source_qual.use_src_qual.src_qual):
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	79 $call_control.source_qual.use_src_qual.src_qual
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	80 #if $ign_vcfs:
2 dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	81 --ign-vcf '$ign_vcfs'
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	82 #end if
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	83 --def-nm-q $call_control.source_qual.use_src_qual.def_nm_q
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	84 #end if
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	85 --min-jq $call_control.joint_qual.min_jq
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	86 --min-alt-jq $call_control.joint_qual.min_alt_jq
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	87 --def-alt-jq $call_control.joint_qual.def_alt_jq
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	88 #end if
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	89
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	90 --sig $filter_control.sig
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	91 #set $bonf_factor = $filter_control.bonf or 'dynamic'
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	92 --bonf $bonf_factor
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	93 $filter_control.others
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	94
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	95 reads.bam 2>&1
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	96
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	97 ## in case of errors add the log files produced
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	98 ## by the parallel workers to stderr
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	99 \|\| (tool_exit_code=\$? && cat pp-tmp/lofreq2_call_parallel/.log 1>&2 && exit \$tool_exit_code)
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	100
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	101 ## work around a bug in lofreq call-parallel
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	102 ## https://github.com/CSB5/lofreq/issues/85
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	103 ## that causes the output format to be vcf.gz with certain filter
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	104 ## combinations.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	105 #if str($bonf_factor) != 'dynamic':
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	106 #if '--no-default-filter' in str($filter_control.others):
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	107 && ln -s variants.vcf variants.vcf.gz
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	108 && gzip -df variants.vcf.gz
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	109 #end if
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	110 #end if
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	111 ]]></command>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	112 <inputs>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	113 <param type="data" name="reads" format="bam" label="Input reads in BAM format" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	114 <expand macro="reference_interface" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	115 <conditional name="regions">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	116 <param name="restrict_to_region" type="select"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	117 label="Call variants across">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	118 <option value="genome">Whole reference</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	119 <option value="regions_from_file">Regions specified in BED</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	120 </param>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	121 <when value="genome" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	122 <when value="regions_from_file">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	123 <param argument="--bed" type="data" format="bed"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	124 label="BED dataset with regions to examine" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	125 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	126 </conditional>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	127 <param name="variant_types" type="select"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	128 label="Types of variants to call"
3 3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	129 help="Note: To have indels included in the called variants you HAVE to preprocess your input data using lofreq indelqual to include indel qualities. In addition, it is highly recommended that you calculate and make use of indel alignment qualities. See the detailed tool help below.">
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	130 <option value="--call-indels">SNVs and indels</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	131 <option value="" selected="True">Only SNVs</option>
3 3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	132 <option value="--call-indels --only-indels">Only indels</option>
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	133 </param>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	134 <conditional name="call_control">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	135 <param name="set_call_options" type="select"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	136 label="Variant calling parameters">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	137 <option value="no">Use default settings</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	138 <option value="yes">Configure settings</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	139 </param>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	140 <when value="no" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	141 <when value="yes">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	142 <section name="coverage" title="Coverage" expanded="true">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	143 <param name="min_cov" argument="--min-cov" type="integer" value="1" min="1"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	144 label="Minimal coverage"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	145 help="Do not attempt variant calling at sites that are not covered by at least this number of reads (default: 1)" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	146 <param name="max_depth" argument="--max-depth" type="integer" value="1000000" min="1"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	147 label="Coverage cap"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	148 help="For efficiency, don not consider more than this number of reads at any site (default: 1,000,000)" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	149 </section>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	150 <section name="pe" title="Paired reads" expanded="true">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	151 <param name="use_orphan" argument="--use-orphan" type="boolean" truevalue="--use-orphan" falsevalue="" checked="False"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	152 label="Use reads from anomalously mapped pairs"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	153 help="Applies to paired-end reads only. If set to true, reads from pairs that are flagged as non-proper pairs (SAM/BAM FLAG field 2) will be used in variant calling. The default is to ignore such reads." />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	154 </section>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	155 <section name="bc_quals" title="Base-calling quality" expanded="true">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	156 <param name="min_bq" argument="--min-bq" type="integer" value="6"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	157 label="Minimum baseQ"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	158 help="For variant calling at any given site, do not consider reads for which the base at that site has a base quality less than this value (default: 6)" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	159 <param name="min_alt_bq" argument="--min-alt-bq" type="integer" min="0" value="6"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	160 label="Minimum baseQ for alternate bases"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	161 help="For variant calling at any given site, do not consider reads that support a non-reference allele at the site if that base has a base quality less than this value (default: 6). Note: this setting will have no effect if the specified value is less than the general Minimum baseQ above." />
2 dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	162 <conditional name="alt_bq">
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	163 <param name="modify" type="select"
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	164 label="Base quality to use for alternate bases"
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	165 help="After filtering reads according to the Minimum baseQ settings above, you can choose to modify the base qualities of the non-reference bases in the surviving reads before performing further calculations.">
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	166 <option value="">Use original base qualities</option>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	167 <option value="avg">Use the median of the reference base qualities at the site</option>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	168 <option value="custom">Use a fixed custom value</option>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	169 </param>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	170 <when value="" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	171 <when value="avg">
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	172 <param name="def_alt_bq" type="hidden" value="-1" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	173 </when>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	174 <when value="custom">
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	175 <param name="def_alt_bq" argument="--def-alt-bq" type="integer" min="1" value="1"
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	176 label="Overwrite original base qualities with this value" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	177 </when>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	178 </conditional>
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	179 </section>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	180 <section name="align_quals" title="Base alignment quality" expanded="true"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	181 help="Choose here whether you want to incorporate base and/or indel alignment qualities into lofreq's joint quality model. If you have previously computed and stored (using lofreq alnqual) any of these quality scores into your input dataset, you can tell the tool to reuse them. Alternatively, the tool can calculate the necessary scores on the fly.">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	182 <conditional name="alnqual">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	183 <param name="use_alnqual" type="select"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	184 label="Consider base/indel alignment qualities during variant calling?">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	185 <option value="">Yes, and prefer existing alignment qualities encoded in input</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	186 <option value="--del-baq">Yes, (re)calculate alignment qualities on the fly and use them</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	187 <option value="-A -B">No, don't make use of alignment qualities</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	188 </param>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	189 <when value="">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	190 <expand macro="handle_existing_alnqual" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	191 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	192 <when value="--del-baq">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	193 <expand macro="handle_alnqual" mode="Add and use" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	194 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	195 <when value="-A -B" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	196 </conditional>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	197 </section>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	198 <section name="map_quals" title="Mapping quality" expanded="true">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	199 <param name="min_mq" argument="--min-mq" type="integer" value="0"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	200 label="Minimum mapping quality"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	201 help="For variant calling at any given site, do not consider reads with a mapping quality (MAPQ) less than this value (default: 0 = do not filter on read mapping quality)." />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	202 <conditional name="use_mq">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	203 <param name="no_mq" argument="--no-mq" type="select"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	204 label="Consider mapping quality during variant calling?">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	205 <option value="">Yes, incorporate MAPQ into joint quality score</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	206 <option value="--no-mq">No, ignore MAPQ scores during variant calling</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	207 </param>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	208 <when value="">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	209 <param name="max_mq" argument="--max-mq" type="integer" value="255"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	210 label="Maximum mapping quality"
2 dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	211 help="For the joint quality model at any site, cap the mapping quality of reads at this value (default: 255 = do not cap mapping qualities). Notes: 1) You cannot cap mapping qualities at less than the minimum MAPQ defined above. If you try, MAPQs will be capped at that minimum quality instead. 2) The special MAPQ value 255 is used by many tools to indicate undefined mapping quality, and lofreq call will ignore such reads during variant calling. Capping, however, will turn 255 into a regular MAPQ score. Thus, if you need to avoid using such reads, you should filter out MAPQ 255 reads from your input data with other tools before using lofreq call with MAPQ capping."/>
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	212 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	213 <when value="--no-mq">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	214 <param name="max_mq" type="hidden" value="" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	215 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	216 </conditional>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	217 </section>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	218 <section name="source_qual" title="Source quality" expanded="true">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	219 <conditional name="use_src_qual">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	220 <param argument="--src-qual" name="src_qual" type="select"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	221 label="Compute source quality and consider it during variant calling">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	222 <option value="">No, don't incorporate source quality into joint quality score</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	223 <option value="--src-qual">Yes, compute source quality and merge it into joint quality score</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	224 </param>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	225 <when value="" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	226 <when value="--src-qual">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	227 <param name="def_nm_q" argument="--def-nm-q" type="integer" min="-1" value="-1"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	228 label="Replace non-match base qualities with this value"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	229 help="For the calculation of the source quality, replace all base qualities of non-match bases with this value (default: -1 = use original base qualities)." />
2 dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	230 <param name="ign_vcf" argument="--ign-vcf" type="data" format="vcf,vcf_bgzip" optional="true" multiple="true"
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	231 label="VCF input(s) with variants to ignore for source quality computation"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	232 help="Mismatches caused by known true variants in your samples should not lower the source quality estimate. If any read in your input has a base that is non-reference, but supports one of the known variants in the specified VCF datasets, that base will not be treated as a mismatch." />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	233 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	234 </conditional>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	235 </section>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	236 <section name="joint_qual" title="Joint quality" expanded="true">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	237 <param name="min_jq" argument="--min-jq" type="integer" min="0" value="0"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	238 label="Minimum joinedQ"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	239 help="At any site, do not use reads for variant calling, if their calculated joint quality at that site is lower than this value (default: 0 = do not filter based on joint quality)" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	240 <param name="min_alt_jq" argument="--min-alt-jq" type="integer" min="0" value="0"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	241 label="Minimum joinedQ for alternate bases"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	242 help="At any site, do not use reads for variant calling, if they support a non-reference allele at that site and their calculated joint quality at the site is lower than this value (default: 0 = do not filter based on joint quality). Note: this setting has no effect if the specified value is smaller than the general Minimum joinedQ set above." />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	243 <!-- def-alt-jq==-1, though documented, is currently not implemented -->
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	244 <param name="def_alt_jq" argument="--def-alt-jq" type="integer" min="0" value="0"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	245 label="Overwrite joinedQs of alternate bases with this value"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	246 help="After filtering according to the Minimum joinedQ settings above, set the joint quality values for all reads surviving filtering and supporting a non-reference allele to this value (default: 0 = use the original calculated joint quality)." />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	247 </section>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	248 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	249 </conditional>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	250 <conditional name="filter_control">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	251 <param name="filter_type" type="select"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	252 label="Variant filter parameters">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	253 <option value="set_all_off">Strictly no filtering</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	254 <option value="set_no_default">Preset QUAL score-based filtering</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	255 <option value="set_lofreq_standard" selected="true">Preset filtering on QUAL score + coverage + strand bias (lofreq call default)</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	256 <option value="set_custom">Custom filter settings/combinations</option>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	257 </param>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	258 <when value="set_all_off">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	259 <param name="sig" type="hidden" value="1" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	260 <param name="bonf" type="hidden" value="1" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	261 <param name="others" type="hidden" value="--no-default-filter" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	262 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	263 <when value="set_no_default">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	264 <param name="sig" type="hidden" value="0.01" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	265 <param name="bonf" type="hidden" value="dynamic" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	266 <param name="others" type="hidden" value="--no-default-filter" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	267 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	268 <when value="set_lofreq_standard">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	269 <param name="sig" type="hidden" value="0.01" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	270 <param name="bonf" type="hidden" value="dynamic" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	271 <param name="others" type="hidden" value="" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	272 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	273 <when value="set_custom">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	274 <param name="sig" type="float" value="0.01" min="0" max="1"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	275 label="Significance threshold for calls"/>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	276 <param name="bonf" type="integer" value="0" min="0"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	277 label="Bonferroni correction factor for multiple testing"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	278 help="Set to zero to determine dynamically from actual number of variant tests performed. Dynamic detection will calculate separate correction factors for SNVs and indels" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	279 <param name="others" type="boolean" truevalue="" falsevalue="--no-default-filter" checked="true"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	280 label="Apply default coverage and strand-bias filter?"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	281 help="" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	282 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	283 </conditional>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	284 </inputs>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	285 <outputs>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	286 <data name="variants" from_work_dir="variants.vcf" format="vcf" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	287 </outputs>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	288 <tests>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	289 <test>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	290 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	291 <param name="ref_selector" value="history" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	292 <param name="ref" ftype="fasta" value="pBR322.fa" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	293 <output name="variants" file="call-out1.vcf" lines_diff="4" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	294 </test>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	295 <test>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	296 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	297 <param name="ref_selector" value="history" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	298 <param name="ref" ftype="fasta" value="pBR322.fa" />
2 dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	299 <conditional name="call_control">
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	300 <param name="set_call_options" value="yes" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	301 </conditional>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	302 <output name="variants" file="call-out1.vcf" lines_diff="4" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	303 </test>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	304 <test>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	305 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	306 <param name="ref_selector" value="history" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	307 <param name="ref" ftype="fasta" value="pBR322.fa" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	308 <conditional name="call_control">
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	309 <param name="set_call_options" value="yes" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	310 <section name="source_qual">
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	311 <conditional name="use_src_qual">
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	312 <param name="src_qual" value="--src-qual" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	313 <param name="def_nm_q" value="40" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	314 <param name="ign_vcf" ftype="vcf" value="call-out1.vcf" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	315 </conditional>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	316 </section>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	317 </conditional>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	318 <output name="variants" file="call-out1.vcf" lines_diff="4" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	319 </test>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	320 <test>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	321 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	322 <param name="ref_selector" value="history" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" iuc parents: 0 diff changeset	323 <param name="ref" ftype="fasta" value="pBR322.fa" />
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	324 <conditional name="filter_control">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	325 <param name="filter_type" value="set_all_off" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	326 </conditional>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	327 <output name="variants" file="call-out2.vcf" lines_diff="4" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	328 </test>
3 3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	329 <test>
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	330 <param name="reads" ftype="bam" value="indelqual-out3.bam" />
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	331 <param name="ref_selector" value="history" />
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	332 <param name="ref" ftype="fasta" value="pBR322.fa" />
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	333 <param name="variant_types" value="--call-indels --only-indels" />
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	334 <conditional name="filter_control">
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	335 <param name="filter_type" value="set_all_off" />
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	336 </conditional>
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	337 <output name="variants" file="indel-call-out.vcf" lines_diff="4" />
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	338 </test>
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	339 </tests>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	340 <help><![CDATA[
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	341 lofreq call: call variants from BAM file
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	342
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	343 LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	344 from next-generation sequencing data. It makes full use of base-call qualities
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	345 and other sources of errors inherent in sequencing, which are usually ignored
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	346 by other methods or only used for filtering.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	347
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	348 LoFreq can run on almost any type of aligned sequencing data since no machine-
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	349 or sequencing-technology dependent thresholds are used. It automatically adapts
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	350 to changes in coverage and sequencing quality and can therefore be applied to a
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	351 variety of data-sets e.g. viral/quasispecies, bacterial, metagenomics or
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	352 somatic data.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	353
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	354 While the tool will often give reasonable results with default settings a
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	355 variety of options let you control its exact behavior. These advanced options
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	356 can be subdivided into those affecting variant calling and those affecting
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	357 posterior filtering of the results.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	358
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	359 Variant calling paramters
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	360
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	361 At the heart of LoFreq's variant caller is a joint quality score that is
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	362 computed for every site in every read (that survives filtering) and that
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	363 combines some or all of the following read and base quality measures:
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	364
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	365 - Base/indel quality
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	366
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	367 For any read, this is the Phred-scaled likelihood that the base mapped to a
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	368 given site does not represent a sequencing error. For every base, this score
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	369 got computed by the base caller of your sequencing platform and got
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	370 incorporated into your input dataset during read alignment.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	371
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	372 For insertions/deletions this is defined, analogously, as the Phred-scaled
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	373 likelihood that any inserted/deleted base is real, however, you are
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	374 responsible for adding indel qualitites, which are required for indel
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	375 calling with lofreq, to your input.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	376
3 3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1" iuc parents: 2 diff changeset	377 For doing so, you can use ``lofreq indelqual``.
0 31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	378
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	379 - Base/indel alignment quality
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	380
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	381 For any read, this is the Phred-scaled likelihood that the read's base or
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	382 indel mapped to a given reference genome position is mapped to this position
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	383 correctly.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	384
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	385 The tool can calculate these scores for you on the fly. Alternatively, you
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	386 can precalculate them using ``lofreq alnqual``, which will incorporate them
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	387 into your input dataset.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	388
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	389 - Mapping quality
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	390
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	391 The Phred-scaled likelihood that the read got mapped to the correct place
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	392 in the reference genome. This score got incorporated into your input dataset
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	393 by the aligner you used to map your reads.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	394
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	395 - Source quality
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	396
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	397 This is the Phred-scaled likelihood that the given read comes from the
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	398 reference genome. The tool can calculate this score for you.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	399
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	400
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	401 Variant filter parameters
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	402
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	403 After generating a list of called variants, the tool can filter this list
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	404 based on:
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	405
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	406 - the statistical significance of the variant calls
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	407 - strand-bias of reads supporting the variant
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	408 - coverage of the variant site
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	409
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	410 While posterior filtering can help reduce false-positive variant calls, please
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	411 note that the separate ``lofreq filter``, which can be run on the output of
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	412 ``lofreq call`` has many more options for configuring filters.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	413
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	414 These are the different filter settings supported by the tool:
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	415
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	416 Preset filtering on QUAL score + coverage + strand bias
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	417
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	418 For variants to pass this filter, the following is required:
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	419
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	420 - statistical signficance of the variant call with a pvalue < 0.01 based on the
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	421 retransformed QUAL score of the variant and multiple-testing corrected using
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	422 a dynamically determined Bonferroni factor (based on the number of overall
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	423 variants considered during calling).
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	424
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	425 - A strand-bias in supporting reads not significant under a FDR-corrected p
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	426 value of 0.001 and 85% of supporting reads mapped to the same strand of the
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	427 genome.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	428
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	429 - A coverage of the variant site of at least 10x.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	430
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	431 Preset QUAL score-based filtering
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	432
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	433 Same QUAL-based significance filter as the default, but without the strand-bias
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	434 and coverage criteria
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	435
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	436 Strictly no filtering
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	437
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	438 Do not apply any filters, but produce the original list of all called variants.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	439 You will almost always want to use ``lofreq filter`` to process the resulting
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	440 output.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	441
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	442 Custom filter settings/combinations
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	443
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	444 Lets you define your own QUAL-based significance filter and, optionally,
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	445 combine it with the default starnd-bias and coverage filters.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	446 ]]></help>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	447 <expand macro="citations" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60" iuc parents: diff changeset	448 </tool>

Mercurial > repos > iuc > lofreq_call

annotate lofreq_call.xml @ 5:65432c3abf6c draft