Mercurial > repos > jdv > nanopolish

annotate nanopolish_variants.xml @ 6:36cc4ae4160e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d47b131af7d3a9f8446732f91ec08503c99aab58
author jdv
date Mon, 04 Dec 2017 02:03:21 -0500
parents ee4a11ebe451
children 32cb27adeb34
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1 <tool id="nanopolish_variants" name="Nanopolish::variants" version="0.8.2">
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3 <description>Re-call consensus and variants from raw signal</description>
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5 <!-- ***************************************************************** -->
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7 <!--
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8 <requirements>
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9 <requirement type="package" version="0.7.2">nanopolish</requirement>
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10 </requirements>
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11 -->
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13 <!-- ***************************************************************** -->
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15 <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command>
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17 <!-- ***************************************************************** -->
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19 <command detect_errors="aggressive">
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20 <![CDATA[
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22 ln -s $input_bam 'input.bam' &&
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23 ln -s $input_bam.metadata.bam_index input.bai &&
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25 perl $__tool_directory__/nanopolish_variants.pl variants
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27 --reads $input_reads
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28 --bam input.bam
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29 --genome $input_ref
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30 --consensus $out_consensus
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31 --outfile $out_variants
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32 --threads \${GALAXY_SLOTS:-1}
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33 --max-rounds $max_rounds
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34 --max-haplotypes $max_haplotypes
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35 --min-candidate-depth $min_candidate_depth
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36 --min-candidate-frequency $min_candidate_frequency
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37 --fast5 $input_fast5
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38 $fix_homopolymers
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39 $calculate_all_support
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41 ]]>
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42 </command>
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44 <!-- ***************************************************************** -->
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46 <inputs>
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48 <param name="input_reads" type="data" format="fasta" label="Input reads (FASTA)" />
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49 <param name="input_fast5" type="data" format="fast5.tar" label="Input reads (FAST5)" />
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50 <param name="input_bam" type="data" format="bam" label="Alignment" />
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51 <param name="input_ref" type="data" format="fasta" label="Reference" />
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52 <param name="min_candidate_frequency" type="float" value="0.2" size="5" label="Minimum candidate frequency" />
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53 <param name="min_candidate_depth" type="integer" min="1" value="20" size="5" label="Minimum candidate depth" />
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54 <param name="max_haplotypes" type="integer" min="0" value="1000" size="5" label="Maximum haplotype combinations" />
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55 <param name="max_rounds" type="integer" min="0" value="50" size="5" label="Maximum iterations" />
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56 <param name="fix_homopolymers" type="boolean" checked="false" truevalue="--fix-homopolymers" falsevalue="" label="Fix homopolymers" />
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57 <param name="calculate_all_support" type="boolean" checked="false" truevalue="--calculate-all-support" falsevalue="" label="Calculate support for all four bases" />
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58 </inputs>
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60 <!-- ***************************************************************** -->
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62 <outputs>
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64 <data name="out_variants" format="vcf" label="${tool.name} on ${on_string} (variants)" />
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65 <data name="out_consensus" format="fasta" label="${tool.name} on ${on_string} (consensus)" />
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67 </outputs>
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69 <!-- ***************************************************************** -->
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71 <tests>
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72 <test>
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73 <param name="input_reads" value="variants.reads.fa" ftype="fasta" />
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74 <param name="input_fast5" value="variants.in.fast5.tar.bz2" ftype="fast5.tar.bz2" />
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75 <param name="input_bam" value="variants.bam" ftype="bam" />
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76 <param name="input_ref" value="variants.ref.fa" ftype="fasta" />
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77 <param name="fix_homopolymers" value="True"/>
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78 <output name="out_consensus" file="variants.out.fa" compare="diff" />
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79 </test>
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80 </tests>
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82 <!-- ***************************************************************** -->
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84 <help>
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85 <![CDATA[
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87 **Description**
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88
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89 Nanopolish is a software package for signal-level analysis of Oxford Nanopore
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90 sequencing data. Nanopolish can calculate an improved consensus sequence for a
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91 draft genome assembly, detect base modifications, call SNPs and indels with
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92 respect to a reference genome and more.
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93
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94 The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
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95 as input, such as can be produced by `poretools combine`, and always outputs a
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96 single FASTQ file.
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97
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98 This is the `variants` module.
0
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99
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100 ]]>
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101 </help>
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102
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103 <!-- ***************************************************************** -->
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104
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105 <citations>
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106 </citations>
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107
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108 </tool>