Mercurial > repos > iuc > lofreq_call

annotate lofreq_call.xml @ 4:074d44697036 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
author iuc
date Fri, 29 May 2020 15:23:20 -0400
parents 3b4b2121842f
children 65432c3abf6c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents: 2
diff changeset
1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy2">
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>