Mercurial > repos > iuc > genomescope

annotate genomescope.xml @ 1:3169a38c2656 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
author iuc
date Sat, 26 Jun 2021 14:17:47 +0000
parents b2f674562a18
children 01210c4e9144
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3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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1 <tool id="genomescope" name="GenomeScope" version="@VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
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2 <description>reference-free genome profiling</description>
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3 <macros>
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4 <token name="@VERSION@">2.0</token>
1
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5 <token name="@SUFFIX_VERSION@">1</token>
0
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@VERSION@">genomescope2</requirement>
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9 </requirements>
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10 <version_command>genomescope2 --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 genomescope2
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13 --input '$input'
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14 --output .
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15 --kmer_length $kmer_length
1
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16 $output_options.no_unique_sequence
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17 $advanced_options.testing
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18 $advanced_options.trace_flag
0
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19 #if $ploidy:
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20 --ploidy $ploidy
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21 #end if
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22 #if $lambda:
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23 --lambda $lambda
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24 #end if
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25 #if $max_kmercov:
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26 --max_kmercov $max_kmercov
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27 #end if
1
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28 #if $advanced_options.topology:
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29 --topology $advanced_options.topology
0
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30 #end if
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31 #if $advanced_options.initial_repetitiveness:
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32 --initial_repetitiveness $advanced_options.initial_repetitiveness
0
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33 #end if
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34 #if $advanced_options.initial_heterozygosities:
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35 --initial_heterozygosities '${advanced_options.initial_heterozygosities}'
0
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36 #end if
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37 #if $advanced_options.transform_exp:
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38 --transform_exp $advanced_options.transform_exp
0
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39 #end if
1
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40 #if $advanced_options.true_params:
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41 --true_params '${advanced_options.true_params}'
0
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42 #end if
1
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43 #if $advanced_options.num_rounds:
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44 --num_rounds $advanced_options.num_rounds
0
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45 #end if
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46 ]]>
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47 </command>
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48 <inputs>
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49 <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."/>
1
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50 <param argument="--ploidy" type="integer" min="1" max="6" optional="true" label="Ploidy for model to use" help="Default: 2"/>
0
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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"/>
1
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52 <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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53 <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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54 <section name="output_options" title="Output options" expanded="true">
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55 <param name="output_files" type="select" multiple="true" display="checkboxes" label="Output files">
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56 <option value="model_output">Generate a file with the model parameters</option>
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57 <option value="summary_output">Summary of the analysis</option>
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58 <option value="progress_output">Additional information for each optimization round</option>
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59 </param>
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60 <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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61 </section>
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62 <section name="advanced_options" title="Advanced options">
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63 <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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64 <param argument="--initial_repetitiveness" type="float" min="0" max="1" optional="true" label="Initial value for repetitiveness"/>
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65 <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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66 <sanitizer>
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67 <valid initial="string.digits"><add value="," /><add value="." /></valid>
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68 </sanitizer>
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69 <validator type="regex">[0-9,.]+</validator>
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70 </param>
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71 <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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72 <param argument="--testing" type="boolean" truevalue="--testing" falsevalue="" label="Create testing.tsv file with model parameters"/>
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73 <param argument="--true_params" type="text" optional="true" label="Set true simulated parameters for testing mode">
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74 <sanitizer>
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75 <valid initial="string.digits"><add value="," /><add value="." /></valid>
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76 </sanitizer>
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77 <validator type="regex">[0-9,.]+</validator>
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78 </param>
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79 <param argument="--trace_flag" type="boolean" truevalue="--trace_flag" falsevalue="" label="Turn on printing of iteration progress of nlsLM function"/>
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80 <param argument="--num_rounds" type="integer" min="1" optional="true" label="Number of optimization rounds"/>
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81 </section>
0
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82 </inputs>
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83 <outputs>
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84 <data name="linear_plot" format="png" from_work_dir="linear_plot.png" label="${tool.name} on ${on_string} Linear plot"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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85 <data name="log_plot" format="png" from_work_dir="log_plot.png" label="${tool.name} on ${on_string} Log plot"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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86 <data name="transformed_linear_plot" format="png" from_work_dir="transformed_linear_plot.png" label="${tool.name} on ${on_string} Transformed linear plot"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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87 <data name="transformed_log_plot" format="png" from_work_dir="transformed_log_plot.png" label="${tool.name} on ${on_string} Transformed log plot"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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88 <data name="model" format="txt" from_work_dir="model.txt" label="${tool.name} on ${on_string} Model">
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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89 <filter>output_options['output_files'] and 'model_output' in output_options['output_files']</filter>
0
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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90 </data>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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91 <data name="summary" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string} Summary">
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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92 <filter>output_options['output_files'] and 'summary_output' in output_options['output_files']</filter>
0
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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93 </data>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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94 <data name="progress" format="txt" from_work_dir="progress.txt" label="${tool.name} on ${on_string} Progress">
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
95 <filter>output_options['output_files'] and 'progress_output' in output_options['output_files']</filter>
0
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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96 </data>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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97 <data name="model_params" format="tabular" from_work_dir="SIMULATED_testing.tsv" label="${tool.name} on ${on_string} Model parameters">
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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98 <filter>advanced_options['testing']</filter>
0
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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99 </data>
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100 </outputs>
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101 <tests>
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102 <test expect_num_outputs="8">
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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103 <param name="input" value="genomescope-in1.tab"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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diff changeset
104 <param name="kmer_length" value="21"/>
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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105 <section name="output_options">
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
106 <param name="output_files" value="model_output,summary_output,progress_output"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
107 </section>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
108 <section name="advanced_options">
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
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diff changeset
109 <param name="testing" value="true"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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110 </section>
0
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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111 <output name="linear_plot" file="genomescope-out1-1.png" ftype="png"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
112 <output name="log_plot" file="genomescope-out1-2.png" ftype="png"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
113 <output name="transformed_linear_plot" file="genomescope-out1-3.png" ftype="png"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
114 <output name="transformed_log_plot" file="genomescope-out1-4.png" ftype="png" compare="sim_size"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
115 <output name="model" file="genomescope-out1-1.txt" ftype="txt" lines_diff="2"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
116 <output name="summary" file="genomescope-out1-2.txt" ftype="txt" lines_diff="2"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
117 <output name="progress" file="genomescope-out1-3.txt" ftype="txt" lines_diff="2"/>
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
118 <output name="model_params" file="genomescope-out1-1.tab" ftype="tabular"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
119 </test>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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120 <!--Test initial_repetitiveness option-->
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
121 <test expect_num_outputs="5">
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
122 <param name="input" value="genomescope-in1.tab"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
123 <param name="kmer_length" value="21"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
124 <section name="advanced_options">
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
125 <param name="initial_repetitiveness" value="0.1"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
126 </section>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
127 <section name="output_options">
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
128 <param name="output_files" value="summary_output"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
129 </section>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
130 <output name="linear_plot" ftype="png">
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
131 <assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
132 <has_size value="223370" delta="300"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
133 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
134 </output>
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iuc
parents: 0
diff changeset
135 <output name="log_plot" ftype="png">
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
136 <assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
137 <has_size value="201425" delta="300"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
138 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
139 </output>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
140 <output name="transformed_linear_plot" ftype="png">
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
141 <assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
142 <has_size value="221442" delta="300"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
143 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
144 </output>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
145 <output name="transformed_log_plot" ftype="png">
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
146 <assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
147 <has_size value="210889" delta="300"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
148 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
149 </output>
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iuc
parents: 0
diff changeset
150 <output name="summary" ftype="txt" lines_diff="2">
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
151 <assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
152 <has_line line="initial repetitiveness = 0.1"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
153 <has_text text="Homozygous (aa) 98.9538% 98.967%"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
154 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
155 </output>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
156 </test>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
157 <!--Test initial_heterozigosity option-->
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
158 <test expect_num_outputs="5">
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
159 <param name="input" value="genomescope-in1.tab"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
160 <param name="kmer_length" value="21"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
161 <param name="ploidy" value="3"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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162 <section name="advanced_options">
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163 <param name="initial_heterozygosities" value="0.04,0.01"/>
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164 </section>
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165 <section name="output_options">
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166 <param name="output_files" value="summary_output"/>
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167 </section>
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168 <output name="linear_plot" ftype="png">
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169 <assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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170 <has_size value="213366" delta="300"/>
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171 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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172 </output>
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173 <output name="log_plot" ftype="png">
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174 <assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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175 <has_size value="218425" delta="300"/>
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176 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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177 </output>
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178 <output name="transformed_linear_plot" ftype="png">
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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179 <assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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180 <has_size value="217280" delta="300"/>
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181 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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182 </output>
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183 <output name="transformed_log_plot" ftype="png">
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184 <assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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185 <has_size value="229021" delta="300"/>
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186 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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187 </output>
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188 <output name="summary" ftype="txt" lines_diff="2">
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189 <assert_contents>
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190 <has_line line="initial heterozygosities = 0.04,0.01"/>
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191 <has_text text="Homozygous (aaa) 6.03606% 100%"/>
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192 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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193 </output>
0
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194 </test>
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195 </tests>
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196 <help><![CDATA[
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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197
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198 GenomeScope 2.0: Reference-free profiling of polyploid genomes
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199 ==============================================================
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200
1
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201 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
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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202 unassembled sequencing data.
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203
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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204 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.
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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205
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206 -----
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207
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208 .. class:: infomark
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209
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210 **Topological relationships**
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211
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212 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.
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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213
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214 For ploidies of 4 and greater, there are multiple possible topologies. For example, the two tetraploid topologies are:
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215
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216 ::
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217
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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218 AAAA → AAAB → AABC → ABCD
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219 AAAA → AABB → AABC → ABCD
0
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220
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221 ]]></help>
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222 <citations>
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223 <citation type="doi">10.1093/bioinformatics/btx153</citation>
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224 <citation type="doi">10.1038/s41467-020-14998-3</citation>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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225 </citations>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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226 </tool>