Mercurial > repos > jdv > nanopolish

annotate nanopolish_variants.xml @ 12:f64b148e6189 draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit ba4c46d7717e3acd346c9c6bf0bbc9bbecccc190
author jdv
date Fri, 09 Mar 2018 21:56:08 -0500
parents c00a942cfc0b
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1 <tool id="nanopolish_variants" name="Nanopolish::variants" version="0.8.5">
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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 <requirements>
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8 <requirement type="package" version="0.8.5">nanopolish</requirement>
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9 </requirements>
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11 <!-- ***************************************************************** -->
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13 <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command>
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15 <!-- ***************************************************************** -->
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17 <command detect_errors="aggressive">
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18 <![CDATA[
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20 ln -s $input_bam 'input.bam' &&
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21 ln -s $input_bam.metadata.bam_index input.bai &&
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23 perl $__tool_directory__/nanopolish_variants.pl variants
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25 --reads $input_reads
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26 --bam input.bam
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27 --genome $input_ref
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28 --consensus $out_consensus
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29 --outfile $out_variants
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30 --threads \${GALAXY_SLOTS:-1}
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31 --max-rounds $max_rounds
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32 --max-haplotypes $max_haplotypes
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33 --min-candidate-depth $min_candidate_depth
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34 --min-candidate-frequency $min_candidate_frequency
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35 --fast5 $input_fast5
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36 #if $input_index:
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37 --index $input_index
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38 #end if
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39 $fix_homopolymers
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40 $calculate_all_support
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42 ]]>
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43 </command>
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45 <!-- ***************************************************************** -->
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47 <inputs>
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48
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49 <param name="input_reads" type="data" format="fasta,fastq" label="Input reads (FASTA/Q)" />
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50 <param name="input_fast5" type="data" format="fast5.tar" label="Input reads (FAST5)" />
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51 <param name="input_bam" type="data" format="bam" label="Alignment" />
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52 <param name="input_ref" type="data" format="fasta" label="Reference" />
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53 <param name="input_index" type="data" format="tar" label="Precalculated index (optional)" optional="True" />
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54 <param name="min_candidate_frequency" type="float" value="0.2" size="5" label="Minimum candidate frequency" />
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55 <param name="min_candidate_depth" type="integer" min="1" value="20" size="5" label="Minimum candidate depth" />
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56 <param name="max_haplotypes" type="integer" min="0" value="1000" size="5" label="Maximum haplotype combinations" />
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57 <param name="max_rounds" type="integer" min="0" value="50" size="5" label="Maximum iterations" />
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58 <param name="fix_homopolymers" type="boolean" checked="false" truevalue="--fix-homopolymers" falsevalue="" label="Fix homopolymers" />
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59 <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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60 </inputs>
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62 <!-- ***************************************************************** -->
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64 <outputs>
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66 <data name="out_variants" format="vcf" label="${tool.name} on ${on_string} (variants)" />
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67 <data name="out_consensus" format="fasta" label="${tool.name} on ${on_string} (consensus)" />
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69 </outputs>
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71 <!-- ***************************************************************** -->
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73 <tests>
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74 <!-- test defaults with FASTA input -->
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75 <test>
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76 <param name="input_reads" value="called.fa" ftype="fasta" />
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77 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
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78 <param name="input_bam" value="called.bam" ftype="bam" />
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79 <param name="input_ref" value="ref.fa" ftype="fasta" />
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80 <param name="fix_homopolymers" value="False"/>
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81 <output name="out_consensus" file="consensus.fa" compare="diff" />
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82 <output name="out_variants" file="consensus.vcf" compare="diff" />
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83 <assert_command>
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84 <not_has_text text="--index" />
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85 <not_has_text text="--fix-homopolymers" />
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86 </assert_command>
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87 </test>
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88 <!-- test FASTQ input -->
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89 <test>
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90 <param name="input_reads" value="called.fq" ftype="fastq" />
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91 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
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92 <param name="input_bam" value="called.bam" ftype="bam" />
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93 <param name="input_ref" value="ref.fa" ftype="fasta" />
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94 <param name="fix_homopolymers" value="False"/>
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95 <output name="out_consensus" file="consensus.fa" compare="diff" />
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96 <output name="out_variants" file="consensus.vcf" compare="diff" />
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97 </test>
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98 <!-- test homopolymer fixing -->
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99 <test>
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100 <param name="input_reads" value="called.fa" ftype="fasta" />
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101 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
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102 <param name="input_bam" value="called.bam" ftype="bam" />
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103 <param name="input_ref" value="ref.fa" ftype="fasta" />
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104 <param name="fix_homopolymers" value="True"/>
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105 <output name="out_consensus" file="consensus.hp.fa" compare="diff" />
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106 <output name="out_variants" file="consensus.hp.vcf" compare="diff" />
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107 <assert_command>
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108 <has_text text="--fix-homopolymers" />
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109 <not_has_text text="--calculate-all-support" />
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110 </assert_command>
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111 </test>
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112 <!-- test pre-calculated index input, fix-homopolymers command -->
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113 <test>
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114 <param name="input_reads" value="called.fa" ftype="fasta" />
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115 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
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116 <param name="input_bam" value="called.bam" ftype="bam" />
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117 <param name="input_ref" value="ref.fa" ftype="fasta" />
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118 <param name="input_index" value="index.tar" ftype="tar" />
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119 <param name="fix_homopolymers" value="True"/>
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120 <output name="out_consensus" file="consensus.hp.fa" compare="diff" />
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121 <output name="out_variants" file="consensus.hp.vcf" compare="diff" />
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122 <assert_command>
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123 <has_text text="--index" />
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124 </assert_command>
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125 </test>
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126 <!-- test calculate-all-support command -->
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127 <test>
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128 <param name="input_reads" value="called.fa" ftype="fasta" />
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129 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
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130 <param name="input_bam" value="called.bam" ftype="bam" />
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131 <param name="input_ref" value="ref.fa" ftype="fasta" />
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132 <param name="input_index" value="index.tar" ftype="tar" />
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133 <param name="calculate_all_support" value="True"/>
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134 <assert_command>
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135 <not_has_text text="--fix-homopolymers" />
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136 <has_text text="--calculate-all-support" />
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137 </assert_command>
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138 </test>
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139 <!-- test empty input (should return empty output, not throw error) -->
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140 <!-- currently empty inputs don't work, so this test is disabled
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141 <test>
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142 <param name="input_reads" value="called.fa" ftype="fasta" />
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143 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
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144 <param name="input_bam" value="called.bam" ftype="bam" />
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145 <param name="input_ref" value="ref_empty.fa" ftype="fasta" />
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146 <param name="input_index" value="index.tar" ftype="tar" />
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147 <output name="out_consensus" file="consensus.empty.fa" compare="diff" />
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148 <output name="out_variants" file="consensus.empty.vcf" compare="diff" />
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149 </test>
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150 -->
0
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151 </tests>
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152
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153 <!-- ***************************************************************** -->
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154
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155 <help>
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156 <![CDATA[
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157
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158 **Description**
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159
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160 Nanopolish is a software package for signal-level analysis of Oxford Nanopore
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161 sequencing data. Nanopolish can calculate an improved consensus sequence for a
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162 draft genome assembly, detect base modifications, call SNPs and indels with
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163 respect to a reference genome and more.
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164
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165 The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
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166 as input, such as can be produced by `poretools combine`, and always outputs a
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167 single FASTQ file.
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168
3
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169 This is the `variants` module.
0
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170
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171 ]]>
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172 </help>
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174 <!-- ***************************************************************** -->
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176 <citations>
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177 </citations>
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179 </tool>