Mercurial > repos > bgruening > nanopolish_variants

annotate nanopolish_variants.xml @ 4:de5b3d8f5b90 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 25c22b467760e4784e199125292927bd2274a189-dirty
author bgruening
date Sun, 23 Jun 2019 06:04:27 -0400
parents bc79b5b0fe04
children 63af3144371a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
de5b3d8f5b90 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 25c22b467760e4784e199125292927bd2274a189-dirty
bgruening
parents: 3
diff changeset
1 <tool id="nanopolish_variants" name="Nanopolish variants" version="0.11.1">
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
2 <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</description>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
3 <macros>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
4 <import>macros.xml</import>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
5 </macros>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
6 <expand macro="requirements" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
8 ln -s '$input_merged' reads.fasta &&
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
9
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
10 #if $input_reads_raw.extension == 'fast5':
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
11 mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
3
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
12
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
13 #else if $input_reads_raw.extension == 'fast5.tar':
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
14 ln -s '$input_reads_raw' fast5_files.tar &&
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
15 mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files &&
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
16
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
17 #else if $input_reads_raw.extension == 'fast5.tar.bz2':
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
18 ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
19 mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files &&
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
20
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
21 #else:
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
22 ln -s '$input_reads_raw' fast5_files.tar.gz &&
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
23 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
3
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
24
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
25 #end if
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
26
3
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
27 nanopolish index
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
28 -d fast5_files/
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
29 #if $adv.input_seq_summary:
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
30 -s '$adv.input_seq_summary'
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
31 #end if
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
32 reads.fasta &&
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
33
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
34 ln -s '$b' reads.bam &&
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
35 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
1
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
36 #if $reference_source.reference_source_selector == 'history':
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
37 ln -f -s '$reference_source.ref_file' genome.fa &&
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
38 #else:
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
39 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
40 #end if
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
41
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
42 nanopolish variants
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
43 -r reads.fasta
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
44 -b reads.bam
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
45 -g genome.fa
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
46 -o variants.vcf
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
47 #if $consensus:
3
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
48 --consensus
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
49 #end if
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
50
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
51 $snps
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
52 $verbose
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
53 $homopolymer
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
54 $faster
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
55 $all_bases
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
56
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
57 -m $min_candidate_frequency
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
58 -d $min_candidate_depth
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
59 -x $max_haplotypes
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
60 --max-rounds $max_rounds
1
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
61 --threads "\${GALAXY_SLOTS:-4}"
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
62 #if str($min_flanking_sequence):
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
63 --min-flanking-sequence $min_flanking_sequence
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
64 #end if
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
65 #if $ploidy != -1:
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
66 --ploidy $ploidy
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
67 #end if
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
68
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
69 #if $w and str($w).strip():
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
70 -w "${w}"
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
71 #end if
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
72 #if $methylation_aware and str($methylation_aware).strip():
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
73 -q "${methylation_aware}"
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
74 #end if
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
75
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
76 #if $adv.input_events_bam:
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
77 -e '$adv.input_events_bam'
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
78 #end if
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
79 #if $adv.input_genotype:
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
80 --genotype '$adv.input_genotype'
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
81 #end if
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
82 #if $adv.input_candidates:
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
83 -c '$adv.input_candidates'
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
84 #end if
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
85 #if $adv.input_alt_bc_bam:
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
86 -a '$adv.input_alt_bc_bam'
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
87 #end if
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
88 #if $adv.input_models_fofn:
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
89 --models-fofn '$input_models_fofn'
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
90 #end if
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
91
3
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
92 &&
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
93
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
94 nanopolish vcf2fasta --skip-checks -g genome.fa variants.vcf > polished.fa
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
95
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
96
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
97 ]]></command>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
98 <inputs>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
99 <!-- index inputs -->
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
100 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
4
de5b3d8f5b90 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 25c22b467760e4784e199125292927bd2274a189-dirty
bgruening
parents: 3
diff changeset
101 <param type="data" name="input_reads_raw" format="fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
102
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
103 <!-- variants consensus inputs -->
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
104 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
1
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
105 <conditional name="reference_source">
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
106 <param name="reference_source_selector" type="select" label="Load reference genome from">
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
107 <option value="cached">Local cache</option>
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
108 <option value="history">History</option>
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
109 </param>
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
110 <when value="cached">
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
111 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
112 <options from_data_table="all_fasta">
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
113 </options>
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
114 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
115 </param>
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
116 </when>
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
117 <when value="history">
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
118 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
119 </when>
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
120 </conditional>
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
121
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
122 <section name="adv" title="Optional data inputs">
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
123 <!-- optional inputs -->
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
124 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
125 <param type="data" name="input_events_bam" format="bam" optional="true" label="Events aligned to the reference genome" help="(-e)" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
126 <param type="data" name="input_genotype" format="vcf" optional="true" label="Call genotypes for the variants in the vcf file" help="(--genotype)" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
127 <param type="data" name="input_candidates" format="vcf" optional="true"
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
128 label="Use variant candidates, rather than discovering them from aligned reads" help="(-c)" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
129 <param type="data" name="input_alt_bc_bam" format="bam" optional="true" label="Alternative basecaller used that does not output event annotations" help="(-a)" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
130 <param type="data" name="input_models_fofn" format="txt" optional="true" label="Read alternative k-mer models" help="(--models-fofn)" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
131 </section>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
132
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
133 <!-- optional params -->
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
134 <!-- optional params -->
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
135 <param argument="-w" type="text" optional="true"
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
136 label="find variants in window of region chromsome:start-end" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
137 <param name="methylation_aware" type="text" optional="true" label="methylation aware polishing and test motifs given" help="(-q)"/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
138 <param name="min_candidate_frequency" type="float" optional="true" value="0.2" label="Extarct if the variant frequency is at least F" help="(-m)"/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
139 <param name="min_candidate_depth" type="integer" optional="true" value="20" label="Extarct if the depth is at least D" help="(-d)"/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
140 <param name="max_haplotypes" type="integer" optional="true" value="1000" label="Consider at most N haplotype combinations" help="(-x)"/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
141 <param name="max_rounds" type="integer" optional="true" value="50" label="Perform N rounds of consensus sequence improvement" help="(--max_rounds)"/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
142 <param name="ploidy" type="integer" optional="true" value="-1" label="The ploidy level of the sequenced genome. -1:disabled" help="(-p)"/>
1
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
143 <param name="min_flanking_sequence" type="integer" optional="true" value="" label="Distance from alignment end to calculate variants" help="(--min-flanking-sequence)"/>
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
144
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
145 <!-- optional flags -->
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
146 <param argument="--consensus" type="boolean" truevalue="--consensus" falsevalue="" checked="true" label="Consensus calling mode and output polished sequence" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
147 <param argument="--snps" type="boolean" truevalue="--snps" falsevalue="" checked="false" label="only call SNPs"/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
148 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="verbose output"/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
149 <param name="homopolymer" type="boolean" argument="--fix-homopolymers" truevalue="--fix-homopolymers" falsevalue="" checked="false" label="homopolymer caller" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
150 <param argument="--faster" type="boolean" truevalue="--faster" falsevalue="" checked="false"
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
151 label="speedup while slightly reducing consensus accuracy"/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
152 <param name="all_bases" type="boolean" argument="--calculate-all-support" truevalue="--calculate-all-support" falsevalue="" checked="false"
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
153 label="calculate the support of the 3 other possible bases" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
154 </inputs>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
155
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
156 <outputs>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
157 <!-- variants consensus outputs -->
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
158 <data name="output_polished" format="fasta" from_work_dir="polished.fa" label="polished sequence by consensus calling mode" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
159 <data name="output_variants" format="vcf" from_work_dir="variants.vcf" label="Computed variants"/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
160 </outputs>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
161 <tests>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
162 <test>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
163 <param name="input_merged" ftype="fasta" value="reads.fasta" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
164 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
165 <param name="b" value="reads.sorted.bam" />
1
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
166 <param name="reference_source_selector" value="history" />
3
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
167 <param name="ref_file" value="draft_single_seq.fa" />
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
168 <param name="w" value="tig00000001:200000-202000" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
169 <output name="output_polished" file="polished.fa" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
170 <output name="output_variants" file="variants.vcf"/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
171 </test>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
172 <test>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
173 <param name="input_merged" ftype="fasta" value="reads.fasta" />
3
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
174 <param name="input_reads_raw" ftype="fast5.tar.bz2" value="fast5_files.tar.bz2" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
175 <param name="b" value="reads.sorted.bam" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
176 <param name="reference_source_selector" value="history" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
177 <param name="ref_file" value="draft_single_seq.fa" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
178 <param name="w" value="tig00000001:200000-202000" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
179 <output name="output_polished" file="t3_polished.fa" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
180 <output name="output_variants" file="t3_variants.vcf"/>
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
181 </test>
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
182 <test>
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
183 <param name="input_merged" ftype="fasta" value="reads.fasta" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
184 <param name="input_reads_raw" ftype="fast5.tar" value="fast5_files.tar" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
185 <param name="b" value="reads.sorted.bam" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
186 <param name="reference_source_selector" value="history" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
187 <param name="ref_file" value="draft_single_seq.fa" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
188 <param name="w" value="tig00000001:200000-202000" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
189 <output name="output_polished" file="t4_polished.fa" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
190 <output name="output_variants" file="t4_variants.vcf"/>
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
191 </test>
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
192 <test>
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
193 <param name="input_merged" ftype="fasta" value="reads.fasta" />
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
194 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
195 <param name="b" value="reads.sorted.bam" />
1
1ebed8b65752 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents: 0
diff changeset
196 <param name="reference_source_selector" value="history" />
3
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
197 <param name="ref_file" value="draft_single_seq.fa" />
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
198 <param name="w" value="tig00000001:198000-202000" />
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
199 <param name="ploidy" value="2" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
200 <param name="snps" value="true" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
201 <param name="faster" value="true" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
202 <param name="all_bases" value="true" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
203 <param name="consensus" value="false" />
3
bc79b5b0fe04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 1
diff changeset
204 <param name="min_flanking_sequence" value="10" />
0
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
205 <output name="output_polished" file="t2-polished.fa" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
206 <output name="output_variants" file="t2-variants.vcf"/>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
207 </test>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
208 </tests>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
209 <help><![CDATA[
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
210
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
211 Build an index mapping from basecalled reads to the signals measured by the sequencer
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
212 and
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
213 Find SNPs using a signal-level HMM
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
214
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
215 Tutorial and manual available at:
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
216 http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
217
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
218
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
219 ]]></help>
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
220 <expand macro="citations" />
639b3a5bb415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
221 </tool>