Mercurial > repos > galaxy-australia > smudgeplot

annotate smudgeplot.xml @ 5:5a0ddb4dc3a4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 77e22c56f8da58853100ef1be59ba8d077ab1bf4
author iuc
date Thu, 04 May 2023 16:33:09 +0000
parents 5e0825476fb7
children
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5a0ddb4dc3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 77e22c56f8da58853100ef1be59ba8d077ab1bf4
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1 <tool id="smudgeplot" name="Smudgeplot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>inference of ploidy and heterozygosity structure using whole genome sequencing</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
5a0ddb4dc3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 77e22c56f8da58853100ef1be59ba8d077ab1bf4
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7 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 set -o pipefail;
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12 #if $file.input.input_select == 'reads'
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14 ## ~~~~~~~~~~~~~~~ Generate kmer-dump with presets ~~~~~~~~~~~~~~~~~~~~~
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16 ## Jellyfish kmer count
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17 ## ---------------------------------------------------------------------
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19 mkdir -p './files/' &&
5e0825476fb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 72ae2e05f35098c4cb6dd4f038bff07fd36917ed
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20 #if $file.input.reads[0].ext.endswith(".gz")
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21 zcat
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22 #for $f in $file.input.reads
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23 '$f'
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24 #end for
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25 | jellyfish count -m $file.input.mer_len -t \${GALAXY_SLOTS:-8} -s 1M -o 1_counts.jf -C /dev/stdin
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26 #else
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27 jellyfish count -m $file.input.mer_len -t \${GALAXY_SLOTS:-8} -s 1M -o 1_counts.jf -C
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28 #for $f in $file.input.reads
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29 '$f'
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30 #end for
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31 #end if
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33 && jellyfish histo 1_counts.jf > 1_kmer_k21.hist
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35 ## Calculate lower and upper kmer count cutoffs
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36 ## ---------------------------------------------------------------------
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37
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38 #if $file.input.lower_cutoff:
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39 && L=$file.input.lower_cutoff
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40 #else
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41 && L=\$(smudgeplot.py cutoff 1_kmer_k21.hist L)
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42 #end if
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43
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44 #if $file.input.upper_cutoff:
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45 && U=$file.input.upper_cutoff
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46 #else
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47 && U=\$(smudgeplot.py cutoff 1_kmer_k21.hist U)
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48 #end if
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50 ## ---------------------------------------------------------------------
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51 ## Dump and extract coverage
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53 && echo "Dump with cutoffs L=\$L, U=\$U"
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54 && jellyfish dump -c -L \$L -U \$U 1_counts.jf > 2_dump.jf
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55 && smudgeplot.py hetkmers -o 2_kmer_pairs 2_dump.jf
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56
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57
0
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58 #else
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59 #if $file.input.input_mode.selector == 'meryl'
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60 tar -zxf '${file.input.input_mode.meryl_database}' -C ./ &&
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61 #if $file.input.input_mode.lower_cutoff:
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62 L=$file.input.input_mode.lower_cutoff &&
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63 #else
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64 L=\$(smudgeplot.py cutoff '${file.input.input_mode.meryl_histogram}' L) &&
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65 #end if
0
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67 #if $file.input.input_mode.upper_cutoff:
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68 U=$file.input.input_mode.upper_cutoff &&
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69 #else
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70 U=\$(smudgeplot.py cutoff '${file.input.input_mode.meryl_histogram}' U) &&
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71 #end if
0
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72
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73 meryl print less-than \$U greater-than \$L threads=\${GALAXY_SLOTS:-8} memory=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) read-db.meryl | sort > meryl.dump &&
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74 smudgeplot.py hetkmers -o 2_kmer_pairs < meryl.dump
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76 #else
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78 smudgeplot.py hetkmers -o 2_kmer_pairs '$file.input.input_mode.dump'
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79 #end if
0
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81 #end if
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83 ## ---------------------------------------------------------------------
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84 ## Plot
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85
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86 && smudgeplot.py plot $homozygous 2_kmer_pairs_coverages.tsv -o my_genome
0
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87
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88 ]]></command>
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89
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90 <inputs>
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91 <section name="file" title="File inputs" expanded="true">
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92 <conditional name="input">
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93 <param
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94 name="input_select" type="select" label="Select input type"
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95 help="For more control, create your own Kmer dump using Jellyfish.
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96 See Smudgeplot on GitHub for more details: https://github.com/KamilSJaron/smudgeplot"
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97 >
3
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98 <option value="reads" selected="true">Sequencing reads</option>
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99 <option value="dump">Kmer dump file</option>
0
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100 </param>
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101
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102 <when value="reads">
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103 <param
3
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104 name="reads" type="data" format="fastqsanger,fastqsanger.gz,fasta.gz,fasta"
0
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105 label="Sequencing reads" multiple="true"
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106 help="Sequencing reads corresponding to your genome.
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107 Don't worry about read pairing as it is not used in Kmer-counting.
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108 If selecting multiple datasets, please do not mix datatypes!"
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109 />
4
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110
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111 <param argument="--mer-len"
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112 type="integer"
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113 min="1"
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114 value="21"
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115 label="K-mer size"
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116 help="The size of k-mers should be large enough allowing the k-mer to map uniquely to the genome" />
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117
5
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118 <expand macro="cutoff_macro"/>
0
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119
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120 </when>
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121
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122 <when value="dump">
5
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123 <conditional name="input_mode">
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124 <param name="selector" type="select" label="Input mode">
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125 <option value="default">Default k-mer dump dataset</option>
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126 <option value="meryl">Meryl database</option>
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127 </param>
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128 <when value="default">
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129 <param
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130 name="dump" type="data" format="txt"
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131 label="Kmer dump"
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132 help="Upload your own Kmer dump file created with the Jellyfish or KMC tool.
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133 This enables control over kmer-counting parameters."
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134 />
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135 </when>
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136 <when value="meryl">
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137 <param argument="meryl_histogram" type="data" format="tabular" label="Meryl histogram"/>
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138 <param argument="meryl_database" type="data" format="meryldb" label="Meryl database"/>
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139 <expand macro="cutoff_macro"/>
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140 </when>
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141 </conditional>
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142
0
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143 </when>
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144 </conditional>
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145 </section>
4
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146 <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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147
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148 <param name="table_output" type="boolean" label="Output summary table"></param>
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149 <param name="verbose_output" type="boolean" label="Output verbose summary"></param>
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150 <param name="warnings_output" type="boolean" label="Output genome warnings"></param>
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151 </inputs>
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152
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153 <outputs>
3
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154 <data
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155 name="smudgeplot" format="png"
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156 from_work_dir="my_genome_smudgeplot.png"
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157 label="${tool.name} on ${on_string}: Smudgeplot"
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158 />
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159 <data
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160 name="smudgeplot_log" format="png"
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161 from_work_dir="my_genome_smudgeplot_log10.png"
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162 label="${tool.name} on ${on_string}: Smudgeplot (log10)"
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163 />
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164 <data
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165 name="genome_summary" format="tabular"
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166 from_work_dir="my_genome_summary_table.tsv"
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167 label="${tool.name} on ${on_string}: Genome summary table"
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168 >
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169 <filter>table_output</filter>
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170 </data>
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171 <data
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172 name="genome_summary_verbose" format="txt"
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173 from_work_dir="my_genome_verbose_summary.txt"
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174 label="${tool.name} on ${on_string}: Genome verbose summary"
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175 >
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176 <filter>verbose_output</filter>
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177 </data>
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178 <data
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179 name="genome_warnings" format="txt"
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180 from_work_dir="my_genome_warnings.txt"
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181 label="${tool.name} on ${on_string}: Genome warnings"
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182 >
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183 <filter>warnings_output</filter>
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184 </data>
0
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185 </outputs>
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186
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187 <tests>
3
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188 <!-- Standard run -->
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189 <test expect_num_outputs="2">
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190 <param name="input_select" value="reads"/>
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191 <param name="reads" value="test_reads.fasta" ftype="fasta"/>
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192 <param name="lower_cutoff" value="2"/>
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193 <param name="upper_cutoff" value="25"/>
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194 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
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195 </test>
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196 <!-- Standard run with gzipped input -->
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197 <test expect_num_outputs="2">
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198 <param name="input_select" value="reads"/>
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199 <param name="reads" value="test_reads.fasta.gz" ftype="fasta.gz"/>
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200 <param name="lower_cutoff" value="2"/>
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201 <param name="upper_cutoff" value="25"/>
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202 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
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203 </test>
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204 <!-- Multiple input read files -->
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205 <test expect_num_outputs="2">
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206 <param name="input_select" value="reads"/>
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207 <param name="lower_cutoff" value="2"/>
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208 <param name="upper_cutoff" value="80"/>
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209 <param
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210 name="reads"
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211 value="test_reads.fasta,test_reads_2.fasta,test_reads_3.fasta"
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212 ftype="fasta"
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213 />
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214 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
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215 </test>
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216 <!-- With additional outputs-->
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217 <test expect_num_outputs="5">
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218 <param name="input_select" value="reads"/>
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219 <param name="reads" value="test_reads.fasta" ftype="fasta"/>
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220 <param name="lower_cutoff" value="2"/>
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221 <param name="upper_cutoff" value="25"/>
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222 <param name="table_output" value="true"/>
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223 <param name="verbose_output" value="true"/>
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224 <param name="warnings_output" value="true"/>
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225 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
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226 <output name="genome_summary" ftype="tabular" file="my_genome_summary_table.tsv"/>
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227 <output name="genome_summary_verbose" ftype="txt" file="my_genome_verbose_summary.txt"/>
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228 <output name="genome_warnings" ftype="txt" file="my_genome_warnings.txt"/>
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229 </test>
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230 <!-- K-mer dump input -->
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231 <test expect_num_outputs="2">
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232 <param name="input_select" value="dump"/>
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233 <conditional name="input_mode">
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234 <param name="selector" value="default"/>
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235 <param name="dump" value="dump.jf" ftype="txt"/>
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236 </conditional>
3
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237 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
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238 </test>
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239 <!-- Standard run without specifying cutoffs and compressed file -->
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240 <test expect_num_outputs="2">
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241 <param name="input_select" value="reads"/>
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242 <param name="reads" value="test_reads_4.fasta.gz,test_reads_5.fasta.gz"/>
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243 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot_02.png" compare="sim_size"/>
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244 <assert_stdout>
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245 <has_text text="Dump with cutoffs L=10, U=70" />
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246 </assert_stdout>
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247 </test>
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248 <!-- K-mer dump meryl input -->
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249 <test expect_num_outputs="2">
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250 <param name="input_select" value="dump"/>
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251 <conditional name="input_mode">
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252 <param name="selector" value="meryl"/>
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253 <param name="meryl_histogram" value="histogram.tabular" ftype="tabular"/>
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254 <param name="meryl_database" value="kmerdb.meryldb" ftype="meryldb"/>
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255 </conditional>
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256 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot_03.png" compare="sim_size"/>
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257 </test>
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258 <!-- K-mer dump meryl input with specific cutoff-->
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259 <test expect_num_outputs="2">
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260 <param name="input_select" value="dump"/>
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261 <conditional name="input_mode">
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262 <param name="selector" value="meryl"/>
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263 <param name="meryl_histogram" value="histogram.tabular" ftype="tabular"/>
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264 <param name="meryl_database" value="kmerdb.meryldb" ftype="meryldb"/>
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265 <param name="lower_cutoff" value="2"/>
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266 <param name="upper_cutoff" value="2500000"/>
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267 </conditional>
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268 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot_04.png" compare="sim_size"/>
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269 </test>
0
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270 </tests>
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271
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272 <help><![CDATA[
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273
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274 .. class:: infomark
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275
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276 **What it does**
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277
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278 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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279
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280 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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281
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282 .. image:: $PATH_TO_IMAGES/smudge.png
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283 :height: 520
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284 :alt: Example smudgeplot graph
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285
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286 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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287
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288 Please see `Smudgeplot on GitHub <https://github.com/KamilSJaron/smudgeplot>`_
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289 for further documentation and tutorials.
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290
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291 **Inputs**
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292
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293 You have two choices when running Smudgeplot in Galaxy:
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294
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295 1. Input reads file(s) for default kmer-counting with Jellyfish
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296
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297 This should be at least one file which providing coverage of your genome of interest.
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298 The tool accepts compressed (.gz) inputs. If choosing this option, you can
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299 (optionally) specify manual cutoff values for the kmer dump step. The Smudgeplot
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300 docs suggest that you can use GenomeScope on a kmer histogram in order to choose
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301 reasonable lower and upper cutoff values.
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302
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303 2. Input your own kmer dump file for more control of kmer counting parameters
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304
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305 This file would be created by running ``jellyfish count`` and then ``jellyfish dump`` - the process is well described
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306 `on GitHub <https://github.com/KamilSJaron/smudgeplot>`_.
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307
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308 **Outputs**
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309
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310 - ``smudgeplot.png`` smudgeplot image
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311 - ``smudgeplot_log10.png`` smudgeplot with log scale
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312 - ``my_genome_summary.tsv`` summarized genome statistics
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313 - ``my_genome_verbose.txt`` detailed genome statistics
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314 - ``my_genome_warnings.txt`` warnings emitted from the Smudgeplot tool
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315
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316 **Default operation**
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317
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318 If choosing reads as the input, a default kmer counting procedure will be used
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319 to create a kmer dump. This default process is summarized as follows:
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320
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321 - ``jellyfish count -m 21 > counts.jf``
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322 - ``jellyfish histo counts.jf > counts.hist``
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323 - ``smudgeplot.py cutoff counts.hist`` to get kmer cutoff values (U & L)
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324 - ``jellyfish dump -c -L <L> -U <U> counts.jf > dump.jf``
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325
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326 The kmer dump file is then used to create a smudgeplot:
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327
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328 - ``smudgeplot.py hetkmers -o kmer_pairs dump.jf``
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329 - ``smudgeplot.py plot kmer_pairs_coverages.tsv -o my_genome``
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330
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331 ]]></help>
5
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332 <expand macro="citations"/>
0
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333 </tool>