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annotate smudgeplot.xml @ 0:4c91967b3e6d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
author iuc
date Thu, 30 Jun 2022 22:44:50 +0000
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4c91967b3e6d 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">
4c91967b3e6d 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>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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4 <macros>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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5 <token name="@TOOL_VERSION@">0.2.5</token>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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6 <token name="@VERSION_SUFFIX@">1</token>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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7 </macros>
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4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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9 <xrefs>
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10 <xref type="bio.tools">smudgeplots</xref>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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11 </xrefs>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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13 <requirements>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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14 <requirement type="package" version="@TOOL_VERSION@">smudgeplot</requirement>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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15 <requirement type="package" version="2.3.0">kmer-jellyfish</requirement>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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16 </requirements>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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18 <command detect_errors="exit_code"><![CDATA[
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20 #if $file.input.input_select == 'reads'
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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22 ## ~~~~~~~~~~~~~~~ Generate kmer-dump with presets ~~~~~~~~~~~~~~~~~~~~~
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24 ## Jellyfish kmer count
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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25 ## ---------------------------------------------------------------------
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27 #if $file.input.reads[0].is_of_type("fastqsanger.gz") or $file.input.reads[0].is_of_type("fasta.gz")
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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28 gunzip -c
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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29 #for $f in $file.input.reads
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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30 #if $f
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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31 '$f'
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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32 #end if
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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33 | jellyfish count -m 21 -t 4 -s 1M -o 1_counts.jf -C /dev/stdin
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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34 #end for
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35
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36 #else
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37 jellyfish count -m 21 -t 4 -s 1M -o 1_counts.jf -C
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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38 #for $f in $file.input.reads
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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39 #if $f
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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40 '$f'
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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41 #end if
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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42 #end for
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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43 #end if
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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44
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45 && jellyfish histo 1_counts.jf > 1_kmer_k21.hist
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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46
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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47 ## Calculate lower and upper kmer count cutoffs
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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48 ## ---------------------------------------------------------------------
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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49
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50 #if $file.input.lower_cutoff is not None:
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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51 && L=$file.input.lower_cutoff
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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52 #else
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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53 && L=\$(smudgeplot.py cutoff 1_kmer_k21.hist L)
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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54 #end if
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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55
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56 #if $file.input.upper_cutoff is not None:
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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57 && U=$file.input.upper_cutoff
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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58 #else
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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59 && U=\$(smudgeplot.py cutoff 1_kmer_k21.hist U)
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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60 #end if
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61
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62 ## ---------------------------------------------------------------------
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63 ## Dump and extract coverage
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64
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65 && echo "Dump with cutoffs L=\$L, U=\$U"
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66 && jellyfish dump -c -L \$L -U \$U 1_counts.jf > 2_dump.jf
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67 && smudgeplot.py hetkmers -o 2_kmer_pairs 2_dump.jf
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68
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69 #else
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70
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71 ## ~~~~~~~~~~~~~~~~~~~ Use provided kmer dump ~~~~~~~~~~~~~~~~~~~~~~~~~~
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72
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73 smudgeplot.py hetkmers -o 2_kmer_pairs '$file.input.dump'
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74
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75 #end if
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76
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77 ## ---------------------------------------------------------------------
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78 ## Plot
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79
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80 && smudgeplot.py plot 2_kmer_pairs_coverages.tsv -o my_genome
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81
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82 ]]></command>
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83
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84 <inputs>
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85 <section name="file" title="File inputs" expanded="true">
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86 <conditional name="input">
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87 <param
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88 name="input_select" type="select" label="Select input type"
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89 help="For more control, create your own Kmer dump using Jellyfish.
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90 See Smudgeplot on GitHub for more details: https://github.com/KamilSJaron/smudgeplot"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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91 >
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92 <option value="reads" selected="true">Sequencing reads</option>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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93 <option value="dump">Kmer dump file</option>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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94 </param>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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95
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96 <when value="reads">
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97 <param
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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98 name="reads" type="data" format="fastqsanger,fastqsanger.gz,fasta.gz,fasta"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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99 label="Sequencing reads" multiple="true"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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100 help="Sequencing reads corresponding to your genome.
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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101 Don't worry about read pairing as it is not used in Kmer-counting.
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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102 If selecting multiple datasets, please do not mix datatypes!"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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103 />
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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104
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105 <param
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
106 name="lower_cutoff"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
107 label="Lower kmer cutoff"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
108 type="integer"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
109 optional="true"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
110 help="Optionally set a manual lower limit for filtering kmers with
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
111 smudgeplot hetkmers. If no value is set, a cutoff will be
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
112 estimated with smudgeplot cutoff. Use the GenomeScope tool to
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
113 visualize your kmer histogram when choosing cutoff values."
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
114 />
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
115
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
116 <param
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
117 name="upper_cutoff"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
118 label="Upper kmer cutoff"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
119 type="integer"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
120 optional="true"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
121 help="Optionally set a manual upper limit for filtering kmers with
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
122 smudgeplot hetkmers. If no value is set, a cutoff will be
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
123 estimated with smudgeplot cutoff. Use the GenomeScope tool to
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
124 visualize your kmer histogram when choosing cutoff values."
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
125 />
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
126 </when>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
127
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
128 <when value="dump">
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
129 <param
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
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130 name="dump" type="data" format="txt"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
131 label="Kmer dump"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
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132 help="Upload your own Kmer dump file created with the Jellyfish or KMC tool.
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
133 This enables control over kmer-counting parameters."
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
134 />
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
135 </when>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
136 </conditional>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
137 </section>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
138
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
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139 <param name="table_output" type="boolean" label="Output summary table"></param>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
140 <param name="verbose_output" type="boolean" label="Output verbose summary"></param>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
141 <param name="warnings_output" type="boolean" label="Output genome warnings"></param>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
142 </inputs>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
143
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
144 <outputs>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
145 <data
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
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146 name="smudgeplot" format="png"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
147 from_work_dir="my_genome_smudgeplot.png"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
148 label="${tool.name} on ${on_string}: Smudgeplot"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
149 />
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
150 <data
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
151 name="smudgeplot_log" format="png"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
152 from_work_dir="my_genome_smudgeplot_log10.png"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
153 label="${tool.name} on ${on_string}: Smudgeplot (log10)"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
154 />
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
155 <data
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
156 name="genome_summary" format="tabular"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
157 from_work_dir="my_genome_summary_table.tsv"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
158 label="${tool.name} on ${on_string}: Genome summary table"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
159 >
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
160 <filter>table_output</filter>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
161 </data>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
162 <data
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
163 name="genome_summary_verbose" format="txt"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
164 from_work_dir="my_genome_verbose_summary.txt"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
165 label="${tool.name} on ${on_string}: Genome verbose summary"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
166 >
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
167 <filter>verbose_output</filter>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
168 </data>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
169 <data
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
170 name="genome_warnings" format="txt"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
171 from_work_dir="my_genome_warnings.txt"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
172 label="${tool.name} on ${on_string}: Genome warnings"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
173 >
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
174 <filter>warnings_output</filter>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
175 </data>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
176 </outputs>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
177
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
178 <tests>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
179 <!-- Standard run -->
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
180 <test expect_num_outputs="2">
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
181 <param name="input_select" value="reads"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
182 <param name="reads" value="test_reads.fasta" ftype="fasta"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
183 <param name="lower_cutoff" value="2"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
184 <param name="upper_cutoff" value="25"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
185 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
186 </test>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
187 <!-- Standard run with gzipped input -->
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
188 <test expect_num_outputs="2">
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
189 <param name="input_select" value="reads"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
190 <param name="reads" value="test_reads.fasta.gz" ftype="fasta.gz"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
191 <param name="lower_cutoff" value="2"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
192 <param name="upper_cutoff" value="25"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
193 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
194 </test>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
195 <!-- Multiple input read files -->
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
196 <test expect_num_outputs="2">
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
197 <param name="input_select" value="reads"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
198 <param name="lower_cutoff" value="2"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
199 <param name="upper_cutoff" value="80"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
200 <param
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
201 name="reads"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
202 value="test_reads.fasta,test_reads_2.fasta,test_reads_3.fasta"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
203 ftype="fasta"
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
204 />
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
205 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
206 </test>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
207 <!-- With additional outputs-->
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
208 <test expect_num_outputs="5">
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
209 <param name="input_select" value="reads"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
parents:
diff changeset
210 <param name="reads" value="test_reads.fasta" ftype="fasta"/>
4c91967b3e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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211 <param name="lower_cutoff" value="2"/>
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212 <param name="upper_cutoff" value="25"/>
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213 <param name="table_output" value="true"/>
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214 <param name="verbose_output" value="true"/>
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215 <param name="warnings_output" value="true"/>
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216 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
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217 <output name="genome_summary" ftype="tabular" file="my_genome_summary_table.tsv"/>
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218 <output name="genome_summary_verbose" ftype="txt" file="my_genome_verbose_summary.txt"/>
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219 <output name="genome_warnings" ftype="txt" file="my_genome_warnings.txt"/>
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220 </test>
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221 <!-- K-mer dump input -->
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222 <test expect_num_outputs="2">
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223 <param name="input_select" value="dump"/>
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224 <param name="dump" value="dump.jf" ftype="txt"/>
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225 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
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226 </test>
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227 </tests>
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228
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229 <help><![CDATA[
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230
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231 .. class:: infomark
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232
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233 **What it does**
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234
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235 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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236
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237 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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238
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239 .. image:: $PATH_TO_IMAGES/smudge.png
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240 :height: 520
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241 :alt: Example smudgeplot graph
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242
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243 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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244
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245 Please see `Smudgeplot on GitHub <https://github.com/KamilSJaron/smudgeplot>`_
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246 for further documentation and tutorials.
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247
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248 **Inputs**
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249
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250 You have two choices when running Smudgeplot in Galaxy:
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251
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252 1. Input reads file(s) for default kmer-counting with Jellyfish
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253
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254 This should be at least one file which providing coverage of your genome of interest.
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255 The tool accepts compressed (.gz) inputs. If choosing this option, you can
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256 (optionally) specify manual cutoff values for the kmer dump step. The Smudgeplot
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257 docs suggest that you can use GenomeScope on a kmer histogram in order to choose
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258 reasonable lower and upper cutoff values.
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259
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260 2. Input your own kmer dump file for more control of kmer counting parameters
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261
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262 This file would be created by running ``jellyfish count`` and then ``jellyfish dump`` - the process is well described
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263 `on GitHub <https://github.com/KamilSJaron/smudgeplot>`_.
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264
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265 **Outputs**
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266
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267 - ``smudgeplot.png`` smudgeplot image
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268 - ``smudgeplot_log10.png`` smudgeplot with log scale
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269 - ``my_genome_summary.tsv`` summarized genome statistics
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270 - ``my_genome_verbose.txt`` detailed genome statistics
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271 - ``my_genome_warnings.txt`` warnings emitted from the Smudgeplot tool
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272
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273 **Default operation**
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274
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275 If choosing reads as the input, a default kmer counting procedure will be used
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276 to create a kmer dump. This default process is summarized as follows:
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277
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278 - ``jellyfish count -m 21 > counts.jf``
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279 - ``jellyfish histo counts.jf > counts.hist``
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280 - ``smudgeplot.py cutoff counts.hist`` to get kmer cutoff values (U & L)
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281 - ``jellyfish dump -c -L <L> -U <U> counts.jf > dump.jf``
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282
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283 The kmer dump file is then used to create a smudgeplot:
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284
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285 - ``smudgeplot.py hetkmers -o kmer_pairs dump.jf``
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286 - ``smudgeplot.py plot kmer_pairs_coverages.tsv -o my_genome``
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287
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288 ]]></help>
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289 <citations>
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290 <citation type="doi">10.1038/s41467-020-14998-3</citation>
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291 </citations>
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292 </tool>