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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
author iuc
date Wed, 03 Dec 2025 15:37:35 +0000
parents c3a55a02a2d8
children
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73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
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1 <tool id="genomescope" name="GenomeScope" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>reference-free genome profiling</description>
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3 <macros>
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73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
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4 <token name="@TOOL_VERSION@">2.1.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <token name="@PROFILE@">21.01</token>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">genomescope2</requirement>
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10 </requirements>
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11 <version_command>genomescope2 --version</version_command>
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12 <command detect_errors="exit_code"><![CDATA[
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13 genomescope2
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14 --input '$input'
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15 --output .
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16 --kmer_length $kmer_length
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17 $output_options.no_unique_sequence
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18 $advanced_options.testing
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19 $advanced_options.trace_flag
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20 #if $ploidy:
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21 --ploidy $ploidy
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22 #end if
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23 #if $lambda:
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24 --lambda $lambda
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25 #end if
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26 #if $max_kmercov:
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27 --max_kmercov $max_kmercov
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28 #end if
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29 #if $advanced_options.topology:
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30 --topology $advanced_options.topology
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31 #end if
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32 #if $advanced_options.initial_repetitiveness:
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33 --initial_repetitiveness $advanced_options.initial_repetitiveness
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34 #end if
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35 #if $advanced_options.initial_heterozygosities:
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36 --initial_heterozygosities '${advanced_options.initial_heterozygosities}'
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37 #end if
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38 #if $advanced_options.transform_exp:
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39 --transform_exp $advanced_options.transform_exp
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40 #end if
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41 #if $advanced_options.true_params:
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42 --true_params '${advanced_options.true_params}'
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43 #end if
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44 #if $advanced_options.num_rounds:
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45 --num_rounds $advanced_options.num_rounds
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46 #end if
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47 ]]>
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48 </command>
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49 <inputs>
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50 <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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51 <param argument="--ploidy" type="integer" min="1" max="6" optional="true" label="Ploidy for model to use" help="Default: 2"/>
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52 <param argument="--kmer_length" type="integer" value="21" optional="false" label="K-mer length used to calculate k-mer spectra"/>
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53 <param argument="--lambda" type="integer" optional="true" label="Initial k-mer coverage estimate for model to use" help="This parameter is optional"/>
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54 <param argument="--max_kmercov" type="integer" optional="true" label="Maximum k-mer coverage threshold" help="K-mers with coverage greater than max_kmercov are ignored by the model. This parameter is optional"/>
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55 <section name="output_options" title="Output options" expanded="true">
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56 <param name="output_files" type="select" multiple="true" display="checkboxes" label="Output files">
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57 <option value="model_output">Generate a file with the model parameters</option>
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58 <option value="summary_output">Summary of the analysis</option>
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59 <option value="progress_output">Additional information for each optimization round</option>
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60 </param>
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61 <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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62 </section>
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63 <section name="advanced_options" title="Advanced options">
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64 <param argument="--topology" type="integer" optional="true" label="Topological relationships between the homologous chromosomes" help="Flag for topology for model to use. Topology refers to the similarities between distinct homologues. Each triploid topology consists of two nucleotide heterozygosity forms (e.g. aab and abc), while each tetraploid, pentaploid, and hexaploid topology consists of three, four, and five heterozygosity forms respectively."/>
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65 <param argument="--initial_repetitiveness" type="float" min="0" max="1" optional="true" label="Initial value for repetitiveness"/>
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66 <param argument="--initial_heterozygosities" type="text" optional="true" label="Initial values for nucleotide heterozygosity rates" help="Nucleotide hetegozygosity rates should be float values (separated by commas if necessary)">
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67 <sanitizer>
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68 <valid initial="string.digits"><add value="," /><add value="." /></valid>
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69 </sanitizer>
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70 <validator type="regex">[0-9,.]+</validator>
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71 </param>
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72 <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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73 <param argument="--testing" type="boolean" truevalue="--testing" falsevalue="" label="Create testing.tsv file with model parameters"/>
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74 <param argument="--true_params" type="text" optional="true" label="Set true simulated parameters for testing mode">
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75 <sanitizer>
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76 <valid initial="string.digits"><add value="," /><add value="." /></valid>
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77 </sanitizer>
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78 <validator type="regex">[0-9,.]+</validator>
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79 </param>
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80 <param argument="--trace_flag" type="boolean" truevalue="--trace_flag" falsevalue="" label="Turn on printing of iteration progress of nlsLM function"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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81 <param argument="--num_rounds" type="integer" min="1" optional="true" label="Number of optimization rounds"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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82 </section>
0
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
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83 </inputs>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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84 <outputs>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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85 <data name="linear_plot" format="png" from_work_dir="linear_plot.png" label="${tool.name} on ${on_string} Linear plot"/>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
86 <data name="log_plot" format="png" from_work_dir="log_plot.png" label="${tool.name} on ${on_string} Log plot"/>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
87 <data name="transformed_linear_plot" format="png" from_work_dir="transformed_linear_plot.png" label="${tool.name} on ${on_string} Transformed linear plot"/>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
88 <data name="transformed_log_plot" format="png" from_work_dir="transformed_log_plot.png" label="${tool.name} on ${on_string} Transformed log plot"/>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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89 <data name="model" format="txt" from_work_dir="model.txt" label="${tool.name} on ${on_string} Model">
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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90 <filter>output_options['output_files'] and 'model_output' in output_options['output_files']</filter>
0
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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91 </data>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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92 <data name="summary" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string} Summary">
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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93 <filter>output_options['output_files'] and 'summary_output' in output_options['output_files']</filter>
0
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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94 </data>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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diff changeset
95 <data name="progress" format="txt" from_work_dir="progress.txt" label="${tool.name} on ${on_string} Progress">
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
96 <filter>output_options['output_files'] and 'progress_output' in output_options['output_files']</filter>
0
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
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97 </data>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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diff changeset
98 <data name="model_params" format="tabular" from_work_dir="SIMULATED_testing.tsv" label="${tool.name} on ${on_string} Model parameters">
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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99 <filter>advanced_options['testing']</filter>
0
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
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100 </data>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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101 </outputs>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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102 <tests>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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103 <test expect_num_outputs="8">
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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104 <param name="input" value="genomescope-in1.tab"/>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
105 <param name="kmer_length" value="21"/>
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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106 <section name="output_options">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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107 <param name="output_files" value="model_output,summary_output,progress_output"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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108 </section>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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109 <section name="advanced_options">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
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110 <param name="testing" value="true"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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111 </section>
2
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
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112 <output name="linear_plot" ftype="png">
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
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113 <assert_contents>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
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114 <has_size value="223370" delta="6000"/>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
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115 </assert_contents>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
116 </output>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
117 <output name="log_plot" ftype="png">
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
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118 <assert_contents>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
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119 <has_size value="201425" delta="6000"/>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
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120 </assert_contents>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
121 </output>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
122 <output name="transformed_linear_plot" ftype="png">
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
123 <assert_contents>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
124 <has_size value="221442" delta="6000"/>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
125 </assert_contents>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
126 </output>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
127 <output name="transformed_log_plot" ftype="png">
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
128 <assert_contents>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
129 <has_size value="210889" delta="6000"/>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
130 </assert_contents>
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
131 </output>
4
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
132 <output name="model" ftype="txt">
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
133 <assert_contents>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
134 <has_n_lines n="19"/>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
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135 </assert_contents>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
136 </output>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
137 <output name="summary" ftype="txt">
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
138 <assert_contents>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
139 <has_n_lines n="15"/>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
140 </assert_contents>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
141 </output>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
142 <output name="progress" ftype="txt">
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
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143 <assert_contents>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
144 <has_n_lines n="6"/>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
145 </assert_contents>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
146 </output>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
147 <output name="model_params" ftype="tabular">
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
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148 <assert_contents>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
149 <has_n_lines n="1"/>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
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150 </assert_contents>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
151 </output>
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
152 </test>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
153 <!--Test initial_repetitiveness option-->
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
154 <test expect_num_outputs="5">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
155 <param name="input" value="genomescope-in1.tab"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
156 <param name="kmer_length" value="21"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
157 <section name="advanced_options">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
158 <param name="initial_repetitiveness" value="0.1"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
159 </section>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
160 <section name="output_options">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
161 <param name="output_files" value="summary_output"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
162 </section>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
163 <output name="linear_plot" ftype="png">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
164 <assert_contents>
2
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
165 <has_size value="223370" delta="6000"/>
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
166 </assert_contents>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
167 </output>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
168 <output name="log_plot" ftype="png">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
169 <assert_contents>
2
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
170 <has_size value="201425" delta="6000"/>
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
171 </assert_contents>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
172 </output>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
173 <output name="transformed_linear_plot" ftype="png">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
174 <assert_contents>
2
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
175 <has_size value="221442" delta="6000"/>
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
176 </assert_contents>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
177 </output>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
178 <output name="transformed_log_plot" ftype="png">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
179 <assert_contents>
2
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
180 <has_size value="210889" delta="6000"/>
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
181 </assert_contents>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
182 </output>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
183 <output name="summary" ftype="txt" lines_diff="2">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
184 <assert_contents>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
185 <has_line line="initial repetitiveness = 0.1"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
186 <has_text text="Homozygous (aa) 98.9538% 98.967%"/>
4
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
187 <has_n_lines n="15"/>
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
188 </assert_contents>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
189 </output>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
190 </test>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
191 <!--Test initial_heterozigosity option-->
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
192 <test expect_num_outputs="5">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
193 <param name="input" value="genomescope-in1.tab"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
194 <param name="kmer_length" value="21"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
195 <param name="ploidy" value="3"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
196 <section name="advanced_options">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
197 <param name="initial_heterozygosities" value="0.04,0.01"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
198 </section>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
199 <section name="output_options">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
200 <param name="output_files" value="summary_output"/>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
201 </section>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
202 <output name="linear_plot" ftype="png">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
203 <assert_contents>
2
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
204 <has_size value="213366" delta="6000"/>
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
205 </assert_contents>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
206 </output>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
207 <output name="log_plot" ftype="png">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
208 <assert_contents>
2
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
209 <has_size value="218425" delta="6000"/>
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
210 </assert_contents>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
211 </output>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
212 <output name="transformed_linear_plot" ftype="png">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
213 <assert_contents>
2
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
214 <has_size value="217280" delta="6000"/>
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
215 </assert_contents>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
216 </output>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
217 <output name="transformed_log_plot" ftype="png">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
218 <assert_contents>
2
893c98cc8799 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
219 <has_size value="229021" delta="6000"/>
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
220 </assert_contents>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
221 </output>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
222 <output name="summary" ftype="txt" lines_diff="2">
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
223 <assert_contents>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
224 <has_line line="initial heterozygosities = 0.04,0.01"/>
4
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
225 <has_text text="Homozygous (aaa) 5.92481% 100%"/>
73f09aee6a57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope commit eb1dd55c41bf179ad72bdbd5560bd25efa35a0bc
iuc
parents: 3
diff changeset
226 <has_n_lines n="17"/>
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
227 </assert_contents>
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
228 </output>
0
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
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229 </test>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
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230 </tests>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
231 <help><![CDATA[
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
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232
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
233 GenomeScope 2.0: Reference-free profiling of polyploid genomes
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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parents:
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234 ==============================================================
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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235
1
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
236 GenomeScope 2.0 applies classical insights from combinatorial theory to establish a detailed mathematical model of how k-mer frequencies will be distributed in heterozygous and polyploid genomes.It employs a polyploid-aware mixture model that, within seconds, accurately infers genome properties from
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
237 unassembled sequencing data.
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
238
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
239 GenomeScope 2.0 uses the k-mer count distribution, e.g. from KMC or Jellyfish, and produces a report and several informative plots describing the genome properties. We validate the approach on simulated polyploid data created using a generative model with parameters for genome size, heterozygosity, repetitiveness, ploidy, and sequencing coverage, and find GenomeScope 2.0 retains accuracy across a broad range of realistic and extreme parameter values.
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
240
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
241 -----
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
242
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
243 .. class:: infomark
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
244
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
245 **Topological relationships**
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
246
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
247 In the field of phylogenetics, the evolutionary relationships between species are often depicted in a branching diagram known as a phylogenetic tree. In this setting, the topology of the tree refers to the branching structure of the tree. We may also depict the similarities between homologous chromosomes in a branching diagram. In this case, a topology refers to the similarities between distinct homologues.
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
248
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
249 For ploidies of 4 and greater, there are multiple possible topologies. For example, the two tetraploid topologies are:
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
250
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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251 ::
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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253 AAAA → AAAB → AABC → ABCD
ddb4d9c135c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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254 AAAA → AABB → AABC → ABCD
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b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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255
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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256 ]]></help>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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257 <citations>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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258 <citation type="doi">10.1093/bioinformatics/btx153</citation>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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259 <citation type="doi">10.1038/s41467-020-14998-3</citation>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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260 </citations>
b4502c498108 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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261 </tool>