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annotate smudgeplot.xml @ 4:5e0825476fb7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 72ae2e05f35098c4cb6dd4f038bff07fd36917ed
author iuc
date Tue, 04 Apr 2023 17:23:19 +0000
parents 24e471d13fe9
children 5a0ddb4dc3a4
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24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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1 <tool id="smudgeplot" name="Smudgeplot" version="@TOOL_VERSION@+galaxy+@VERSION_SUFFIX@" profile="21.05">
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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2 <description>inference of ploidy and heterozygosity structure using whole genome sequencing</description>
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4 <macros>
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5 <token name="@TOOL_VERSION@">0.2.5</token>
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6 <token name="@VERSION_SUFFIX@">2</token>
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7 </macros>
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9 <xrefs>
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10 <xref type="bio.tools">smudgeplots</xref>
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11 </xrefs>
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13 <requirements>
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14 <requirement type="package" version="@TOOL_VERSION@">smudgeplot</requirement>
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15 <requirement type="package" version="2.3.0">kmer-jellyfish</requirement>
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16 </requirements>
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18 <command detect_errors="exit_code"><![CDATA[
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19 set -o pipefail;
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21 #if $file.input.input_select == 'reads'
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23 ## ~~~~~~~~~~~~~~~ Generate kmer-dump with presets ~~~~~~~~~~~~~~~~~~~~~
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25 ## Jellyfish kmer count
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26 ## ---------------------------------------------------------------------
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27
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28 mkdir -p './files/' &&
5e0825476fb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 72ae2e05f35098c4cb6dd4f038bff07fd36917ed
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29 #if $file.input.reads[0].ext.endswith(".gz")
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30 zcat
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31 #for $f in $file.input.reads
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32 '$f'
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33 #end for
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34 | jellyfish count -m $file.input.mer_len -t \${GALAXY_SLOTS:-8} -s 1M -o 1_counts.jf -C /dev/stdin
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35 #else
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36 jellyfish count -m $file.input.mer_len -t \${GALAXY_SLOTS:-8} -s 1M -o 1_counts.jf -C
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37 #for $f in $file.input.reads
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38 '$f'
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39 #end for
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40 #end if
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42 && jellyfish histo 1_counts.jf > 1_kmer_k21.hist
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44 ## Calculate lower and upper kmer count cutoffs
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45 ## ---------------------------------------------------------------------
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46
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47 #if $file.input.lower_cutoff:
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48 && L=$file.input.lower_cutoff
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49 #else
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50 && L=\$(smudgeplot.py cutoff 1_kmer_k21.hist L)
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51 #end if
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52
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53 #if $file.input.upper_cutoff:
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54 && U=$file.input.upper_cutoff
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55 #else
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56 && U=\$(smudgeplot.py cutoff 1_kmer_k21.hist U)
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57 #end if
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58
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59 ## ---------------------------------------------------------------------
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60 ## Dump and extract coverage
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62 && echo "Dump with cutoffs L=\$L, U=\$U"
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63 && jellyfish dump -c -L \$L -U \$U 1_counts.jf > 2_dump.jf
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64 && smudgeplot.py hetkmers -o 2_kmer_pairs 2_dump.jf
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65
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66 #else
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67
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68 ## ~~~~~~~~~~~~~~~~~~~ Use provided kmer dump ~~~~~~~~~~~~~~~~~~~~~~~~~~
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69
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70 smudgeplot.py hetkmers -o 2_kmer_pairs '$file.input.dump'
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71
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72 #end if
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74 ## ---------------------------------------------------------------------
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75 ## Plot
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76
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77 && smudgeplot.py plot $homozygous 2_kmer_pairs_coverages.tsv -o my_genome
0
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78
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79 ]]></command>
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80
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81 <inputs>
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82 <section name="file" title="File inputs" expanded="true">
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83 <conditional name="input">
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84 <param
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85 name="input_select" type="select" label="Select input type"
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86 help="For more control, create your own Kmer dump using Jellyfish.
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87 See Smudgeplot on GitHub for more details: https://github.com/KamilSJaron/smudgeplot"
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88 >
3
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89 <option value="reads" selected="true">Sequencing reads</option>
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90 <option value="dump">Kmer dump file</option>
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91 </param>
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92
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93 <when value="reads">
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94 <param
3
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95 name="reads" type="data" format="fastqsanger,fastqsanger.gz,fasta.gz,fasta"
0
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96 label="Sequencing reads" multiple="true"
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97 help="Sequencing reads corresponding to your genome.
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98 Don't worry about read pairing as it is not used in Kmer-counting.
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99 If selecting multiple datasets, please do not mix datatypes!"
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100 />
4
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101
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102 <param argument="--mer-len"
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103 type="integer"
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104 min="1"
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105 value="21"
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106 label="K-mer size"
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107 help="The size of k-mers should be large enough allowing the k-mer to map uniquely to the genome" />
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108
0
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109
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110 <param
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111 name="lower_cutoff"
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112 min="1"
0
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113 label="Lower kmer cutoff"
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114 type="integer"
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115 optional="true"
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116 help="Optionally set a manual lower limit for filtering kmers with
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117 smudgeplot hetkmers. If no value is set, a cutoff will be
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118 estimated with smudgeplot cutoff. Use the GenomeScope tool to
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119 visualize your kmer histogram when choosing cutoff values."
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120 />
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121
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122 <param
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123 name="upper_cutoff"
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124 min="1"
0
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125 label="Upper kmer cutoff"
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126 type="integer"
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127 optional="true"
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128 help="Optionally set a manual upper limit for filtering kmers with
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129 smudgeplot hetkmers. If no value is set, a cutoff will be
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130 estimated with smudgeplot cutoff. Use the GenomeScope tool to
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131 visualize your kmer histogram when choosing cutoff values."
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132 />
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133 </when>
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134
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135 <when value="dump">
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136 <param
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137 name="dump" type="data" format="txt"
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138 label="Kmer dump"
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139 help="Upload your own Kmer dump file created with the Jellyfish or KMC tool.
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140 This enables control over kmer-counting parameters."
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141 />
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142 </when>
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143 </conditional>
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144 </section>
4
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145 <param argument="--homozygous" type="boolean" truevalue="--homozygous" falsevalue="" checked="false" label="Homozygous" help="Assume no heterozygosity in the genome - plotting a paralog structure." />
0
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146
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147 <param name="table_output" type="boolean" label="Output summary table"></param>
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148 <param name="verbose_output" type="boolean" label="Output verbose summary"></param>
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149 <param name="warnings_output" type="boolean" label="Output genome warnings"></param>
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150 </inputs>
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151
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152 <outputs>
3
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153 <data
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154 name="smudgeplot" format="png"
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155 from_work_dir="my_genome_smudgeplot.png"
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156 label="${tool.name} on ${on_string}: Smudgeplot"
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157 />
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158 <data
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159 name="smudgeplot_log" format="png"
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160 from_work_dir="my_genome_smudgeplot_log10.png"
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161 label="${tool.name} on ${on_string}: Smudgeplot (log10)"
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162 />
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163 <data
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164 name="genome_summary" format="tabular"
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165 from_work_dir="my_genome_summary_table.tsv"
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166 label="${tool.name} on ${on_string}: Genome summary table"
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167 >
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168 <filter>table_output</filter>
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169 </data>
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170 <data
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171 name="genome_summary_verbose" format="txt"
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172 from_work_dir="my_genome_verbose_summary.txt"
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173 label="${tool.name} on ${on_string}: Genome verbose summary"
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174 >
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175 <filter>verbose_output</filter>
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176 </data>
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177 <data
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178 name="genome_warnings" format="txt"
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179 from_work_dir="my_genome_warnings.txt"
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180 label="${tool.name} on ${on_string}: Genome warnings"
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181 >
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182 <filter>warnings_output</filter>
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183 </data>
0
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184 </outputs>
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185
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186 <tests>
3
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187 <!-- Standard run -->
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188 <test expect_num_outputs="2">
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189 <param name="input_select" value="reads"/>
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190 <param name="reads" value="test_reads.fasta" ftype="fasta"/>
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191 <param name="lower_cutoff" value="2"/>
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192 <param name="upper_cutoff" value="25"/>
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193 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
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194 </test>
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195 <!-- Standard run with gzipped input -->
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196 <test expect_num_outputs="2">
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197 <param name="input_select" value="reads"/>
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198 <param name="reads" value="test_reads.fasta.gz" ftype="fasta.gz"/>
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199 <param name="lower_cutoff" value="2"/>
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200 <param name="upper_cutoff" value="25"/>
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201 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
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202 </test>
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203 <!-- Multiple input read files -->
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204 <test expect_num_outputs="2">
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205 <param name="input_select" value="reads"/>
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206 <param name="lower_cutoff" value="2"/>
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207 <param name="upper_cutoff" value="80"/>
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208 <param
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209 name="reads"
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210 value="test_reads.fasta,test_reads_2.fasta,test_reads_3.fasta"
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211 ftype="fasta"
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212 />
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213 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
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214 </test>
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215 <!-- With additional outputs-->
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216 <test expect_num_outputs="5">
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217 <param name="input_select" value="reads"/>
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218 <param name="reads" value="test_reads.fasta" ftype="fasta"/>
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219 <param name="lower_cutoff" value="2"/>
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220 <param name="upper_cutoff" value="25"/>
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221 <param name="table_output" value="true"/>
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222 <param name="verbose_output" value="true"/>
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223 <param name="warnings_output" value="true"/>
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224 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
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225 <output name="genome_summary" ftype="tabular" file="my_genome_summary_table.tsv"/>
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226 <output name="genome_summary_verbose" ftype="txt" file="my_genome_verbose_summary.txt"/>
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227 <output name="genome_warnings" ftype="txt" file="my_genome_warnings.txt"/>
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228 </test>
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229 <!-- K-mer dump input -->
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230 <test expect_num_outputs="2">
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231 <param name="input_select" value="dump"/>
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232 <param name="dump" value="dump.jf" ftype="txt"/>
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233 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
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234 </test>
4
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235 <!-- Standard run without specifying cutoffs and compressed file -->
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236 <test expect_num_outputs="2">
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237 <param name="input_select" value="reads"/>
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238 <param name="reads" value="test_reads_4.fasta.gz,test_reads_5.fasta.gz"/>
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239 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot_02.png" compare="sim_size"/>
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240 <assert_stdout>
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241 <has_text text="Dump with cutoffs L=10, U=70" />
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242 </assert_stdout>
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243 </test>
0
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244 </tests>
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245
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246 <help><![CDATA[
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247
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248 .. class:: infomark
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249
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250 **What it does**
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251
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252 This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc.
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253
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254 Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:
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255
3
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256 .. image:: $PATH_TO_IMAGES/smudge.png
0
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257 :height: 520
3
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258 :alt: Example smudgeplot graph
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259
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260 Every haplotype structure has a unique smudge on the graph and the heat of the smudge indicates how frequently the haplotype structure is represented in the genome compared to the other structures. The image above is an ideal case, where the sequencing coverage is sufficient to beautifully separate all the smudges, providing very strong and clear evidence of triploidy.
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261
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262 Please see `Smudgeplot on GitHub <https://github.com/KamilSJaron/smudgeplot>`_
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263 for further documentation and tutorials.
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264
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265 **Inputs**
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266
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267 You have two choices when running Smudgeplot in Galaxy:
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268
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269 1. Input reads file(s) for default kmer-counting with Jellyfish
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270
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271 This should be at least one file which providing coverage of your genome of interest.
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272 The tool accepts compressed (.gz) inputs. If choosing this option, you can
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273 (optionally) specify manual cutoff values for the kmer dump step. The Smudgeplot
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274 docs suggest that you can use GenomeScope on a kmer histogram in order to choose
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275 reasonable lower and upper cutoff values.
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276
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277 2. Input your own kmer dump file for more control of kmer counting parameters
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278
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279 This file would be created by running ``jellyfish count`` and then ``jellyfish dump`` - the process is well described
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280 `on GitHub <https://github.com/KamilSJaron/smudgeplot>`_.
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281
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282 **Outputs**
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283
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284 - ``smudgeplot.png`` smudgeplot image
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285 - ``smudgeplot_log10.png`` smudgeplot with log scale
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286 - ``my_genome_summary.tsv`` summarized genome statistics
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287 - ``my_genome_verbose.txt`` detailed genome statistics
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288 - ``my_genome_warnings.txt`` warnings emitted from the Smudgeplot tool
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289
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290 **Default operation**
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291
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292 If choosing reads as the input, a default kmer counting procedure will be used
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293 to create a kmer dump. This default process is summarized as follows:
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294
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295 - ``jellyfish count -m 21 > counts.jf``
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296 - ``jellyfish histo counts.jf > counts.hist``
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297 - ``smudgeplot.py cutoff counts.hist`` to get kmer cutoff values (U & L)
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298 - ``jellyfish dump -c -L <L> -U <U> counts.jf > dump.jf``
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299
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300 The kmer dump file is then used to create a smudgeplot:
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301
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302 - ``smudgeplot.py hetkmers -o kmer_pairs dump.jf``
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303 - ``smudgeplot.py plot kmer_pairs_coverages.tsv -o my_genome``
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304
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305 ]]></help>
2
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306 <citations>
3
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iuc
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307 <citation type="doi">10.1038/s41467-020-14998-3</citation>
2
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308 </citations>
0
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309 </tool>