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annotate genomescope.xml @ 0:b2f674562a18 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
author iuc
date Fri, 30 Apr 2021 20:21:25 +0000
parents
children 3169a38c2656
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b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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1 <tool id="genomescope" name="GenomeScope" version="@VERSION@" profile="20.01">
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2 <description>Analyze unassembled short reads</description>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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3 <macros>
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4 <token name="@VERSION@">2.0</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">genomescope2</requirement>
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8 </requirements>
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9 <version_command>genomescope2 --version</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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11 genomescope2
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12 --input '$input'
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13 --output .
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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14 --kmer_length $kmer_length
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15 $no_unique_sequence $testing $trace_flag
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16 #if $ploidy:
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17 --ploidy $ploidy
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18 #end if
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19 #if $lambda:
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20 --lambda $lambda
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21 #end if
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22 #if $max_kmercov:
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23 --max_kmercov $max_kmercov
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24 #end if
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25 #if $topology:
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26 --topology $topology
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27 #end if
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28 #if $initial_repetitiveness:
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29 --initial_repetitiveness $initial_repetitiveness
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30 #end if
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31 #if $initial_heterozygosities:
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32 --initial_heterozygosities $initial_heterozygosities
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33 #end if
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34 #if $transform_exp:
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35 --transform_exp $transform_exp
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36 #end if
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37 #if $true_params:
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38 --true_params $true_params
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39 #end if
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40 #if $num_rounds:
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41 --num_rounds $num_rounds
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42 #end if
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43 ]]>
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44 </command>
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45 <inputs>
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46 <param argument="--input" type="data" format="tabular" label="Input histogram file" help="This file is a two column tabular file for example generated with the histo function of Jellyfish."/>
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47 <param name="model_output" type="boolean" label="Add the model parameters to your history"/>
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48 <param name="summary_output" type="boolean" label="Output a summary of the analysis"/>
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49 <param name="progress_output" type="boolean" label="Additional information for each optimization round"/>
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50 <param argument="--ploidy" type="integer" optional="true" label="Ploidy for model to use" help="Default: 2"/>
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51 <param argument="--kmer_length" type="integer" value="21" optional="false" label="K-mer length used to calculate k-mer spectra"/>
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52 <param argument="--lambda" type="integer" optional="true" label="Optional initial kmercov estimate for model to use"/>
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53 <param argument="--max_kmercov" type="integer" optional="true" label="Optional maximum k-mer coverage threshold" help="K-mers with coverage greater than max_kmercov are ignored by the model"/>
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54 <param argument="--no_unique_sequence" type="boolean" truevalue="--no_unique_sequence" falsevalue="" label="Turn off yellow unique sequence line in plots"/>
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55 <param argument="--topology" type="integer" optional="true" label="Flag for topology for model to use"/>
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56 <param argument="--initial_repetitiveness" type="integer" optional="true" label="Initial value for repetitiveness"/>
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57 <param argument="--initial_heterozygosities" type="integer" optional="true" label="Initial values for nucleotide heterozygosity rates"/>
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58 <param argument="--transform_exp" type="integer" optional="true" label="Parameter for the exponent when fitting a transformed (x**transform_exp*y vs. x) k-mer histogram" help="Default: 1"/>
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59 <param argument="--testing" type="boolean" truevalue="--testing" falsevalue="" label="Create testing.tsv file with model parameters"/>
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60 <param argument="--true_params" type="integer" optional="true" label="Flag to state true simulated parameters for testing mode"/>
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61 <param argument="--trace_flag" type="boolean" truevalue="--trace_flag" falsevalue="" label="Turn on printing of iteration progress of nlsLM function"/>
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62 <param argument="--num_rounds" type="integer" min="1" optional="true" label="Number of optimization rounds"/>
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63 </inputs>
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64 <outputs>
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65 <data name="linear_plot" format="png" from_work_dir="linear_plot.png" label="${tool.name} on ${on_string} Linear plot"/>
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66 <data name="log_plot" format="png" from_work_dir="log_plot.png" label="${tool.name} on ${on_string} Log plot"/>
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67 <data name="transformed_linear_plot" format="png" from_work_dir="transformed_linear_plot.png" label="${tool.name} on ${on_string} Transformed linear plot"/>
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68 <data name="transformed_log_plot" format="png" from_work_dir="transformed_log_plot.png" label="${tool.name} on ${on_string} Transformed log plot"/>
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69 <data name="model" format="txt" from_work_dir="model.txt" label="${tool.name} on ${on_string} Model">
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70 <filter>model_output</filter>
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71 </data>
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72 <data name="summary" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string} Summary">
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73 <filter>summary_output</filter>
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74 </data>
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75 <data name="progress" format="txt" from_work_dir="progress.txt" label="${tool.name} on ${on_string} Progress">
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76 <filter>progress_output</filter>
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77 </data>
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78 <data name="model_params" format="tabular" from_work_dir="SIMULATED_testing.tsv" label="${tool.name} on ${on_string} Model parameters">
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79 <filter>testing</filter>
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80 </data>
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81 </outputs>
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82 <tests>
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83 <test expect_num_outputs="8">
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84 <param name="input" value="genomescope-in1.tab"/>
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85 <param name="kmer_length" value="21"/>
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86 <param name="testing" value="true"/>
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87 <param name="model_output" value="true"/>
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88 <param name="summary_output" value="true"/>
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89 <param name="progress_output" value="true"/>
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90 <output name="linear_plot" file="genomescope-out1-1.png" ftype="png"/>
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91 <output name="log_plot" file="genomescope-out1-2.png" ftype="png"/>
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92 <output name="transformed_linear_plot" file="genomescope-out1-3.png" ftype="png"/>
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93 <output name="transformed_log_plot" file="genomescope-out1-4.png" ftype="png" compare="sim_size"/>
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94 <output name="model" file="genomescope-out1-1.txt" ftype="txt" lines_diff="2"/>
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95 <output name="summary" file="genomescope-out1-2.txt" ftype="txt" lines_diff="2"/>
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96 <output name="progress" file="genomescope-out1-3.txt" ftype="txt" lines_diff="2"/>
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97 <output name="testing" file="genomescope-out1-1.tab" ftype="tabular"/>
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98 </test>
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99 </tests>
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100 <help><![CDATA[
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101
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102 GenomeScope 2.0: Reference-free profiling of polyploid genomes
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103 ==============================================================
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104
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105 GenomeScope 2.0 applies classical insights from combinatorial theory to establish
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106 a detailed mathematical model of how k-mer frequencies will be distributed in
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107 heterozygous and polyploid genomes. GenomeScope 2.0 employs a polyploid-aware
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108 mixture model that, within seconds, accurately infers genome properties from
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109 unassembled sequencing data. GenomeScope 2.0 uses the k-mer count distribution,
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110 e.g. from KMC or Jellyfish, and produces a report and several informative plots
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111 describing the genome properties. We validate the approach on simulated polyploid
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112 data created using a generative model with parameters for genome size, heterozygosity,
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113 repetitiveness, ploidy, and sequencing coverage, and find GenomeScope 2.0 retains
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114 accuracy across a broad range of realistic and extreme parameter values. We also
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115 validate GenomeScope 2.0 by analyzing genuine sequence data from 11 diverse
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116 polyploid genomes with known genome characteristics.
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117
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118 ]]></help>
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119 <citations>
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120 <citation type="doi">10.1093/bioinformatics/btx153</citation>
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121 <citation type="doi">10.1038/s41467-020-14998-3</citation>
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122 </citations>
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123 </tool>