Mercurial > repos > bgruening > nanopolish_variants
comparison nanopolish_variants.xml @ 0:639b3a5bb415 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
author | bgruening |
---|---|
date | Wed, 30 May 2018 11:56:35 -0400 |
parents | |
children | 1ebed8b65752 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:639b3a5bb415 |
---|---|
1 <tool id="nanopolish_variants" name="Nanopolish variants" version="0.1.0"> | |
2 <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 ln -s '$input_merged' reads.fasta && | |
9 | |
10 #if $input_reads_raw.extension == 'fast5': | |
11 mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 && | |
12 #else | |
13 ln -s '$input_reads_raw' fast5_files.tar.gz && | |
14 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files && | |
15 #end if | |
16 | |
17 nanopolish index -d fast5_files/ reads.fasta && | |
18 ln -s '$b' reads.bam && | |
19 ln -s '${b.metadata.bam_index}' reads.bam.bai && | |
20 ln -s '$g' genome.fa && | |
21 | |
22 nanopolish variants | |
23 -r reads.fasta | |
24 -b reads.bam | |
25 -g genome.fa | |
26 -o variants.vcf | |
27 #if $consensus: | |
28 --consensus polished.fa | |
29 #end if | |
30 | |
31 $snps | |
32 $verbose | |
33 $homopolymer | |
34 $faster | |
35 $all_bases | |
36 | |
37 -m $min_candidate_frequency | |
38 -d $min_candidate_depth | |
39 -x $max_haplotypes | |
40 --max-rounds $max_rounds | |
41 #if $ploidy != -1: | |
42 --ploidy $ploidy | |
43 #end if | |
44 | |
45 #if $w and str($w).strip(): | |
46 -w "${w}" | |
47 #end if | |
48 #if $methylation_aware and str($methylation_aware).strip(): | |
49 -q "${methylation_aware}" | |
50 #end if | |
51 | |
52 #if $adv.input_events_bam: | |
53 -e '$adv.input_events_bam' | |
54 #end if | |
55 #if $adv.input_genotype: | |
56 --genotype '$adv.input_genotype' | |
57 #end if | |
58 #if $adv.input_candidates: | |
59 -c '$adv.input_candidates' | |
60 #end if | |
61 #if $adv.input_alt_bc_bam: | |
62 -a '$adv.input_alt_bc_bam' | |
63 #end if | |
64 #if $adv.input_models_fofn: | |
65 --models-fofn '$input_models_fofn' | |
66 #end if | |
67 | |
68 | |
69 | |
70 ]]></command> | |
71 <inputs> | |
72 <!-- index inputs --> | |
73 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> | |
74 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/> | |
75 | |
76 <!-- variants consensus inputs --> | |
77 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> | |
78 <param type="data" argument="-g" format="fasta" label="The reference genome"/> | |
79 | |
80 <section name="adv" title="Optional data inputs"> | |
81 <!-- optional inputs --> | |
82 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/> | |
83 <param type="data" name="input_events_bam" format="bam" optional="true" label="Events aligned to the reference genome" help="(-e)" /> | |
84 <param type="data" name="input_genotype" format="vcf" optional="true" label="Call genotypes for the variants in the vcf file" help="(--genotype)" /> | |
85 <param type="data" name="input_candidates" format="vcf" optional="true" | |
86 label="Use variant candidates, rather than discovering them from aligned reads" help="(-c)" /> | |
87 <param type="data" name="input_alt_bc_bam" format="bam" optional="true" label="Alternative basecaller used that does not output event annotations" help="(-a)" /> | |
88 <param type="data" name="input_models_fofn" format="txt" optional="true" label="Read alternative k-mer models" help="(--models-fofn)" /> | |
89 </section> | |
90 | |
91 <!-- optional params --> | |
92 <!-- optional params --> | |
93 <param argument="-w" type="text" optional="true" | |
94 label="find variants in window of region chromsome:start-end" /> | |
95 <param name="methylation_aware" type="text" optional="true" label="methylation aware polishing and test motifs given" help="(-q)"/> | |
96 <param name="min_candidate_frequency" type="float" optional="true" value="0.2" label="Extarct if the variant frequency is at least F" help="(-m)"/> | |
97 <param name="min_candidate_depth" type="integer" optional="true" value="20" label="Extarct if the depth is at least D" help="(-d)"/> | |
98 <param name="max_haplotypes" type="integer" optional="true" value="1000" label="Consider at most N haplotype combinations" help="(-x)"/> | |
99 <param name="max_rounds" type="integer" optional="true" value="50" label="Perform N rounds of consensus sequence improvement" help="(--max_rounds)"/> | |
100 <param name="ploidy" type="integer" optional="true" value="-1" label="The ploidy level of the sequenced genome. -1:disabled" help="(-p)"/> | |
101 | |
102 <!-- optional flags --> | |
103 <param argument="--consensus" type="boolean" truevalue="--consensus" falsevalue="" checked="true" label="Consensus calling mode and output polished sequence" /> | |
104 <param argument="--snps" type="boolean" truevalue="--snps" falsevalue="" checked="false" label="only call SNPs"/> | |
105 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="verbose output"/> | |
106 <param name="homopolymer" type="boolean" argument="--fix-homopolymers" truevalue="--fix-homopolymers" falsevalue="" checked="false" label="homopolymer caller" /> | |
107 <param argument="--faster" type="boolean" truevalue="--faster" falsevalue="" checked="false" | |
108 label="speedup while slightly reducing consensus accuracy"/> | |
109 <param name="all_bases" type="boolean" argument="--calculate-all-support" truevalue="--calculate-all-support" falsevalue="" checked="false" | |
110 label="calculate the support of the 3 other possible bases" /> | |
111 </inputs> | |
112 | |
113 <outputs> | |
114 <!-- variants consensus outputs --> | |
115 <data name="output_polished" format="fasta" from_work_dir="polished.fa" label="polished sequence by consensus calling mode" /> | |
116 <data name="output_variants" format="vcf" from_work_dir="variants.vcf" label="Computed variants"/> | |
117 </outputs> | |
118 <tests> | |
119 <test> | |
120 <!-- index test --> | |
121 <param name="input_merged" ftype="fasta" value="reads.fasta" /> | |
122 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> | |
123 | |
124 <!-- variants consensus test --> | |
125 <param name="b" value="reads.sorted.bam" /> | |
126 <param name="g" value="draft.fa" /> | |
127 <param name="w" value="tig00000001:200000-202000" /> | |
128 | |
129 <output name="output_polished" file="polished.fa" /> | |
130 <output name="output_variants" file="variants.vcf"/> | |
131 </test> | |
132 <test> | |
133 <!-- index test --> | |
134 <param name="input_merged" ftype="fasta" value="reads.fasta" /> | |
135 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> | |
136 | |
137 <!-- variants consensus test --> | |
138 <param name="b" value="reads.sorted.bam" /> | |
139 <param name="g" value="draft.fa" /> | |
140 <param name="w" value="tig00000001:200000-202000" /> | |
141 <param name="ploidy" value="2" /> | |
142 <param name="snps" value="true" /> | |
143 <param name="faster" value="true" /> | |
144 <param name="all_bases" value="true" /> | |
145 <param name="consensus" value="false" /> | |
146 <output name="output_polished" file="t2-polished.fa" /> | |
147 <output name="output_variants" file="t2-variants.vcf"/> | |
148 </test> | |
149 | |
150 </tests> | |
151 <help><![CDATA[ | |
152 | |
153 Build an index mapping from basecalled reads to the signals measured by the sequencer | |
154 and | |
155 Find SNPs using a signal-level HMM | |
156 | |
157 Tutorial and manual available at: | |
158 http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html | |
159 | |
160 | |
161 ]]></help> | |
162 <expand macro="citations" /> | |
163 </tool> |