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comparison nanopolish_variants.xml @ 8:bec636361cfd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
author bgruening
date Thu, 30 Nov 2023 17:57:59 +0000
parents 63af3144371a
children
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7:a3afc5f0a96c 8:bec636361cfd
1 <tool id="nanopolish_variants" name="Nanopolish variants" version="@VERSION@+galaxy0"> 1 <tool id="nanopolish_variants" name="Nanopolish variants" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</description> 2 <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 ln -s '$input_merged' reads.fasta && 8 @PREPROCESS_INPUTS@
9
10 #if $input_reads_raw.extension == 'fast5':
11 mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
12
13 #else if $input_reads_raw.extension == 'fast5.tar':
14 ln -s '$input_reads_raw' fast5_files.tar &&
15 mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files &&
16
17 #else if $input_reads_raw.extension == 'fast5.tar.bz2':
18 ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
19 mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files &&
20
21 #else:
22 ln -s '$input_reads_raw' fast5_files.tar.gz &&
23 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
24
25 #end if
26
27 nanopolish index
28 -d fast5_files/
29 #if $adv.input_seq_summary:
30 -s '$adv.input_seq_summary'
31 #end if
32 reads.fasta &&
33
34 ln -s '$b' reads.bam &&
35 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
36 #if $reference_source.reference_source_selector == 'history':
37 ln -f -s '$reference_source.ref_file' genome.fa &&
38 #else:
39 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
40 #end if
41 9
42 nanopolish variants 10 nanopolish variants
43 -r reads.fasta 11 -r reads.fasta
44 -b reads.bam 12 -b reads.bam
45 -g genome.fa 13 -g genome.fa
87 #end if 55 #end if
88 #if $adv.input_models_fofn: 56 #if $adv.input_models_fofn:
89 --models-fofn '$input_models_fofn' 57 --models-fofn '$input_models_fofn'
90 #end if 58 #end if
91 59
92 && 60 &&
93 61 nanopolish vcf2fasta
94 nanopolish vcf2fasta --skip-checks -g genome.fa variants.vcf > polished.fa 62 --skip-checks
95 63 -g genome.fa
96 64 variants.vcf > polished.fa
97 ]]></command> 65 ]]></command>
98 <inputs> 66 <inputs>
99 <!-- index inputs --> 67 <!-- index inputs -->
100 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> 68 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
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"/> 69 <param type="data" name="input_reads_raw" format="fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
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)" /> 97 <param type="data" name="input_alt_bc_bam" format="bam" optional="true" label="Alternative basecaller used that does not output event annotations" help="(-a)" />
130 <param type="data" name="input_models_fofn" format="txt" optional="true" label="Read alternative k-mer models" help="(--models-fofn)" /> 98 <param type="data" name="input_models_fofn" format="txt" optional="true" label="Read alternative k-mer models" help="(--models-fofn)" />
131 </section> 99 </section>
132 100
133 <!-- optional params --> 101 <!-- optional params -->
134 <!-- optional params -->
135 <param argument="-w" type="text" optional="true" 102 <param argument="-w" type="text" optional="true"
136 label="find variants in window of region chromsome:start-end" /> 103 label="find variants in window of region chromsome:start-end" />
137 <param name="methylation_aware" type="text" optional="true" label="methylation aware polishing and test motifs given" help="(-q)"/> 104 <param name="methylation_aware" type="text" optional="true" label="methylation aware polishing and test motifs given" help="(-q)"/>
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)"/> 105 <param name="min_candidate_frequency" type="float" optional="true" value="0.2" label="Extarct if the variant frequency is at least F" help="(-m)"/>
139 <param name="min_candidate_depth" type="integer" optional="true" value="20" label="Extarct if the depth is at least D" help="(-d)"/> 106 <param name="min_candidate_depth" type="integer" optional="true" value="20" label="Extarct if the depth is at least D" help="(-d)"/>
249 </test> 216 </test>
250 </tests> 217 </tests>
251 <help><![CDATA[ 218 <help><![CDATA[
252 219
253 Build an index mapping from basecalled reads to the signals measured by the sequencer 220 Build an index mapping from basecalled reads to the signals measured by the sequencer
254 and 221 and find SNPs using a signal-level HMM.
255 Find SNPs using a signal-level HMM
256 222
257 Tutorial and manual available at: 223 Tutorial and manual available at:
258 http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html 224 http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html
259 225
260 226