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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit a2dd716a67d60533534269faef8e87e30496bce0
author iuc
date Thu, 14 Nov 2024 07:25:22 +0000
parents 43fffeed243f
children
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1 <tool id="sniffles" name="sniffles" version="@TOOL_VERSION@+galaxy0" profile="23.0">
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2 <description>Structural variation caller using third generation sequencing</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.5.2</token>
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5 </macros>
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6 <xrefs>
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7 <xref type="bio.tools">sniffles</xref>
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">sniffles</requirement>
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11 </requirements>
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12 <version_command>
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13 <![CDATA[ sniffles --version ]]>
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14 </version_command>
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15 <command detect_errors="exit_code">
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16 <![CDATA[
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17 ln -f -s '${input}' input.bam &&
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18 ln -f -s '${input.metadata.bam_index}' input.bam.bai &&
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19 #if str($reference_genome.genome_type_select) != "None":
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20 #if str($reference_genome.genome_type_select) == "indexed":
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21 ln -f -s '${reference_genome.genome.fields.path}' 'reference.fa' &&
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22 #else:
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23 ln -f -s '${reference_genome.genome}' 'reference.fa' &&
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24 #end if
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25 #end if
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26 sniffles
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27 -t \${GALAXY_SLOTS:-2}
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28 -i 'input.bam'
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29 -v '$output'
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30 ## must set allow-overwrite since the new output vcf file exists
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31 --allow-overwrite
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32 #if str($reference_genome.genome_type_select) != "None":
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33 --reference 'reference.fa'
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34 #end if
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35 ## general_options
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36 --minsupport '$general_options.minsupport'
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37 --max-splits-kb '$general_options.maxsplitskb'
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38 --minsvlen '$general_options.minsvlen'
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39 --mapq '$general_options.mapq'
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40 --min-alignment-length '$general_options.minalignmentlength'
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41 #if str($detectlargeins) == "0":
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42 --detect-large-ins '0'
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43 #end if
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44 ## clustering_options
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45 --cluster-binsize '$clustering_options.clusterbinsize'
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46 --cluster-r '$clustering_options.clusterr'
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47 ## advanced_options
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48 $advanced_options.mosaic
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49 ]]>
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50 </command>
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51 <inputs>
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52 <param type="data" name="input" format="bam" label="Input BAM file"/>
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53 <conditional name="reference_genome">
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54 <param name="genome_type_select" type="select" label="Reference genome source is required for deletion SV sequence reporting"
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55 help="Optional: Select None, a built-in or history reference genome fasta">
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56 <option value="None" selected="True">No reference fasta - do not report DEL SV sequence</option>
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57 <option value="indexed">Use a Galaxy server built-in genome</option>
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58 <option value="history">Use a genome fasta file from the current history</option>
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59 </param>
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60 <when value="None">
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61 <param name="genome" type="hidden" value="None"/>
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62 </when>
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63 <when value="indexed">
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64 <param name="genome" type="select" optional="false" label="Select a built in reference genome or custom genome"
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65 help="If not listed, add a custom genome or use a reference genome from the history">
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66 <options from_data_table="all_fasta">
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67 <validator message="No genomes are available " type="no_options"/>
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68 </options>
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69 </param>
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70 </when>
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71 <when value="history">
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72 <param name="genome" type="data" format="fasta" optional="false" label="Select the reference genome fasta from the current history"/>
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73 </when>
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74 </conditional>
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75 <section name="general_options" title="Set general options" expanded="False">
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76 <param argument="--minsupport" type="text" value="auto" label="Minimum Support" help="Minimum number of reads that support a SV. [auto]. Smaller support values -> more SV reported"/>
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77 <param argument="--maxsplitskb" type="float" value="0.1" min="0" label="Maximum Number of Splits per KB" help="Additional number of splits per kilobase read sequence allowed before reads are ignored [0.1]" />
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78 <param argument="--minsvlen" type="integer" value="50" min="2" label="Minimum Length" help="Minimum length of SV to be reported. [50]"/>
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79 <param argument="--mapq" type="integer" value="20" min="0" label="Minimum Mapping Quality" help="Minimum Mapping Quality to consider. [20]"/>
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80 <param argument="--minalignmentlength" type="integer" value="100" min="0" label="Minimum alignment length" help="Reads with alignments shorter than this length (in bp) will be ignored"/>
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81 <param name="detectlargeins" type="boolean" truevalue="1" falsevalue="0" display="radio" checked="true" label="Detect very large insertions spanning multiple reads"
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82 help="This sometimes shows enormous features."/>
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83 </section>
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84 <section name="clustering_options" title="Clustering/phasing and genotyping options" expanded="False">
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85 <param argument="--clusterbinsize" value="100" type="integer" min="0" label="Cluster bin size" help="Initial screening bin size [100]"/>
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86 <param argument="--clusterr" type="float" value="2.5" min="0.0" label="Cluster Multiplier" help="Multiplier for SV start position standard deviation criterion in cluster merging [2.5]"/>
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87 </section>
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88 <section name="advanced_options" title="Advanced options" expanded="False">
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89 <param argument="--mosaic" type="boolean" display="radio" checked="false" truevalue="--mosaic" falsevalue="" label="Mosaic mode" help="Set Sniffles run mode to detect rare, somatic and mosaic SVs (default: False)" />
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90 </section>
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91 </inputs>
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92 <outputs>
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93 <data name="output" format="vcf" label="${tool.name} on ${on_string}"/>
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94 </outputs>
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95 <tests>
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96 <test> <!-- test 1 - standard run -->
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97 <param name="input" value="reads_region.bam"/>
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98 <param name="detectlargeins" value="0"/>
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99 <output name="output" file="expected_output.vcf" lines_diff="4"/>
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100 </test>
1
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101 <test> <!-- test 2 - filter on mapq -->
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102 <param name="input" value="reads_region.bam"/>
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103 <param name="mapq" value="0"/>
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104 <output name="output" file="expected_output2.vcf" lines_diff="4"/>
0
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105 </test>
1
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106 <test> <!-- test 3 min support test -->
0
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107 <param name="input" value="reads_region.bam"/>
1
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108 <param name="minsupport" value="1"/>
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109 <output name="output" file="expected_outcome3.vcf" lines_diff="4"/>
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110 </test>
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111 <test> <!-- test 4 - clustering -->
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112 <param name="input" value="reads_region.bam"/>
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113 <param name="clusterbinsize" value="5"/>
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114 <output name="output" file="expected_outcome4.vcf" lines_diff="4"/>
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115 </test>
1
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116 <test> <!-- test 5 - Advanced - mosaic -->
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117 <param name="input" value="reads_region.bam"/>
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118 <param name="mosaic" value="--mosaic"/>
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119 <output name="output" file="expected_outcome5.vcf" lines_diff="4"/>
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120 </test>
3
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121 <test> <!-- test 6 - reference -->
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122 <param name="input" value="reads_region.bam"/>
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123 <conditional name="reference_genome">
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124 <param name="genome_type_select" value="history"/>
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125 <param name="genome" value="humsamp.fa"/>
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126 <param name="genome.ext" value="fasta"/>
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127 </conditional>
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128 <output name="output" file="expected_outcome6.vcf" lines_diff="4"/>
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129 </test>
0
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130 </tests>
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131 <help>
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132 <![CDATA[
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133 ########
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134 Sniffles
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135 ########
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136
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137 What is Sniffles?
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138 *****************
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139
1
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140 Sniffles is a SV caller for long reads. Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.
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141
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142 SV are larger events on the genome (e.g. deletions, duplications, insertions, inversions and translocations).
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143 Sniffles can detect all of these type and more such as nested SVs (e.g. inversion flanked by deletions or an inverted duplication).
0
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144
4
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145 ----
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146
1
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147 Inputs
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148 ******
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149
1
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150 Known to work with Minimap2 bam as input
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151 Optional reference fasta with matching contig names will allow deletions to be determined.
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152
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153 ----
0
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154
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155 Parameters
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156 **********
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157
4
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158
0
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159 General
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160 -------
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161
1
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162
4
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163 +----------------------------+-------------------------------------------------------------------------+
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164 | Parameter | Description |
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165 +============================+=========================================================================+
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166 | Minimum Support | Minimum number of reads supporting a SV to be reported. Default:auto |
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167 +----------------------------+-------------------------------------------------------------------------+
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168 | Maximum Number of Splits | Maximum number of split segments per kb a read is aligned at before |
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169 | | it is ignored. Default: 7 |
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170 +----------------------------+-------------------------------------------------------------------------+
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171 | Minimum SV Length | Minimum length of SV to be reported. Default: 50bp |
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172 +----------------------------+-------------------------------------------------------------------------+
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173 | Minimum Mapping Quality | Minimum mapping quality of alignment to be taken into account. |
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174 | | Default: 20 |
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175 +----------------------------+-------------------------------------------------------------------------+
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176 | Minimum alignment length | Reads with less length aligned will be ignored. Default 100 |
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177 +----------------------------+-------------------------------------------------------------------------+
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178
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179
0
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180
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181
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182 Clustering Options
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183 ------------------
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184
1
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185
4
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186 +---------------------+------------------------------------------------------------------------+
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187 | Parameter | Description |
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188 +=====================+========================================================================+
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189 | Cluster bin size | Initial cluster bin size. Default 100 |
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190 +---------------------+------------------------------------------------------------------------+
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191 | Cluster Multiplier | Multiplier for SV start position standard deviation criterion in |
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192 | | cluster merging [2.5] |
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193 +---------------------+------------------------------------------------------------------------+
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194
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195
0
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196
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197
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198 Advanced Options
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199 ----------------
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201
4
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202 +-------------+--------------------------------------------------------------------------------+
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203 | Parameter | Description |
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204 +=============+================================================================================+
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205 | Mosaic | Set Sniffles run mode to detect rare, somatic and mosaic SVs (default: False)|
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206 +-------------+--------------------------------------------------------------------------------+
0
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207
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208
4
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209 ----
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210
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211 VCF information fields from the VCF header
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212 ******************************************
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213
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214 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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215 | Field | Type | Description |
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216 +==================+===========+===============================================================================================+
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217 | PRECISE | Flag | Structural variation with precise breakpoints |
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218 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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219 | IMPRECISE | Flag | Structural variation with imprecise breakpoints |
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220 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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221 | MOSAIC | Flag | Structural variation classified as putative mosaic |
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222 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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223 | SVLEN | Integer | Length of structural variation |
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224 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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225 | SVTYPE | String | Type of structural variation |
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226 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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227 | CHR2 | String | Mate chromsome for BND SVs |
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228 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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229 | SUPPORT | Integer| Number of reads supporting the structural variation |
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230 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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231 | SUPPORT_INLINE | Integer| Number of reads supporting an INS/DEL SV (non-split events only) |
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232 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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233 | SUPPORT_LONG | Integer| Number of soft-clipped reads putatively supporting the long insertion SV |
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234 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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235 | END | Integer| End position of structural variation |
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236 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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237 | STDEV_POS | Float | Standard deviation of structural variation start position |
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238 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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239 | STDEV_LEN | Float | Standard deviation of structural variation length |
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240 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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241 | COVERAGE | Float | Coverage near upstream start, center, end, downstream of structural variation |
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242 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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243 | STRAND | String | Strands of supporting reads for structural variant |
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244 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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245 | AC | Integer| Allele count summed up over all samples |
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246 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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247 | SUPP_VEC | String | List of read support for all samples |
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248 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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249 | CONSENSUS_SUP | Integer| Number of reads that support the generated insertion (INS) consensus sequence |
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250 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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251 | RNAMES | String | Names of supporting reads (if enabled with --output-rnames) |
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252 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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253 | AF | Float | Allele Frequency |
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254 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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255 | NM | Float | Mean number of query alignment length adjusted mismatches of supporting reads |
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256 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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257 | PHASE | String | Phasing information derived from supporting reads |
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258 +------------------+-----------+-----------------------------------------------------------------------------------------------+
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259
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260
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261 ----
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262
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263
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264 Source
0
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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265 ******
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266
4
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267 https://github.com/fritzsedlazeck/Sniffles
1
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268
0
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269 ]]>
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270 </help>
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271 <citations>
1
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272 <citation type="doi">10.1038/s41587-023-02024-y</citation>
0
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273 </citations>
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274 </tool>