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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 0d2b1b7f07cf050b76bb905540f382be7e1cd68f
author iuc
date Fri, 02 Aug 2024 15:39:12 +0000
parents 01210c4e9144
children
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01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
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1 <tool id="genomescope" name="GenomeScope" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.01">
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2 <description>reference-free genome profiling</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.0.1</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_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
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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
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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
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28 #if $advanced_options.topology:
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29 --topology $advanced_options.topology
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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
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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}'
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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
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39 #end if
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40 #if $advanced_options.true_params:
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41 --true_params '${advanced_options.true_params}'
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42 #end if
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43 #if $advanced_options.num_rounds:
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44 --num_rounds $advanced_options.num_rounds
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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."/>
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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"/>
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51 <param argument="--kmer_length" type="integer" value="21" optional="false" label="K-mer length used to calculate k-mer spectra"/>
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52 <param argument="--lambda" type="integer" optional="true" label="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"/>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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81 </section>
0
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iuc
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82 </inputs>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
83 <outputs>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
84 <data name="linear_plot" format="png" from_work_dir="linear_plot.png" label="${tool.name} on ${on_string} Linear plot"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
85 <data name="log_plot" format="png" from_work_dir="log_plot.png" label="${tool.name} on ${on_string} Log plot"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
86 <data name="transformed_linear_plot" format="png" from_work_dir="transformed_linear_plot.png" label="${tool.name} on ${on_string} Transformed linear plot"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
87 <data name="transformed_log_plot" format="png" from_work_dir="transformed_log_plot.png" label="${tool.name} on ${on_string} Transformed log plot"/>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
88 <data name="model" format="txt" from_work_dir="model.txt" label="${tool.name} on ${on_string} Model">
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
89 <filter>output_options['output_files'] and 'model_output' in output_options['output_files']</filter>
0
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
90 </data>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
91 <data name="summary" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string} Summary">
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
92 <filter>output_options['output_files'] and 'summary_output' in output_options['output_files']</filter>
0
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
93 </data>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
94 <data name="progress" format="txt" from_work_dir="progress.txt" label="${tool.name} on ${on_string} Progress">
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
95 <filter>output_options['output_files'] and 'progress_output' in output_options['output_files']</filter>
0
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
96 </data>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
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diff changeset
97 <data name="model_params" format="tabular" from_work_dir="SIMULATED_testing.tsv" label="${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
diff changeset
98 <filter>advanced_options['testing']</filter>
0
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
99 </data>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
100 </outputs>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
101 <tests>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
102 <test expect_num_outputs="8">
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
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"
iuc
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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
diff changeset
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
parents: 0
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
diff changeset
110 </section>
2
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
111 <output name="linear_plot" ftype="png">
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
112 <assert_contents>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
113 <has_size value="223370" delta="6000"/>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
114 </assert_contents>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
115 </output>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
116 <output name="log_plot" ftype="png">
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
117 <assert_contents>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
118 <has_size value="201425" delta="6000"/>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
119 </assert_contents>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
120 </output>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
121 <output name="transformed_linear_plot" ftype="png">
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
122 <assert_contents>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
123 <has_size value="221442" delta="6000"/>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
124 </assert_contents>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
125 </output>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
126 <output name="transformed_log_plot" ftype="png">
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
127 <assert_contents>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
128 <has_size value="210889" delta="6000"/>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
129 </assert_contents>
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
130 </output>
0
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
iuc
parents:
diff changeset
131 <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
parents:
diff changeset
132 <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
parents:
diff changeset
133 <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
134 <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
135 </test>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
136 <!--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
137 <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
138 <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
139 <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
140 <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
141 <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
142 </section>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
143 <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
144 <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
145 </section>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
146 <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
147 <assert_contents>
2
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
148 <has_size value="223370" delta="6000"/>
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
149 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
150 </output>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
151 <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
152 <assert_contents>
2
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
153 <has_size value="201425" delta="6000"/>
1
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 <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
157 <assert_contents>
2
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
158 <has_size value="221442" delta="6000"/>
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
159 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
160 </output>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
161 <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
162 <assert_contents>
2
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
diff changeset
163 <has_size value="210889" delta="6000"/>
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
diff changeset
164 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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parents: 0
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165 </output>
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166 <output name="summary" ftype="txt" lines_diff="2">
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parents: 0
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167 <assert_contents>
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iuc
parents: 0
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168 <has_line line="initial repetitiveness = 0.1"/>
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169 <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"
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170 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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171 </output>
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iuc
parents: 0
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172 </test>
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173 <!--Test initial_heterozigosity option-->
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iuc
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174 <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
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175 <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
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176 <param name="kmer_length" value="21"/>
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177 <param name="ploidy" value="3"/>
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178 <section name="advanced_options">
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179 <param name="initial_heterozygosities" value="0.04,0.01"/>
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180 </section>
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181 <section name="output_options">
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182 <param name="output_files" value="summary_output"/>
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183 </section>
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184 <output name="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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parents: 0
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185 <assert_contents>
2
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
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186 <has_size value="213366" delta="6000"/>
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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187 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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parents: 0
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188 </output>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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parents: 0
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189 <output name="log_plot" ftype="png">
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iuc
parents: 0
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190 <assert_contents>
2
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
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191 <has_size value="218425" delta="6000"/>
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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192 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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parents: 0
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193 </output>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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parents: 0
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194 <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
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195 <assert_contents>
2
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
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196 <has_size value="217280" delta="6000"/>
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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197 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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parents: 0
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198 </output>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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parents: 0
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199 <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
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200 <assert_contents>
2
01210c4e9144 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 41cbd9e93c32d81132ad0ee4dfa606ea67446bb0
iuc
parents: 1
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201 <has_size value="229021" delta="6000"/>
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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202 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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203 </output>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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204 <output name="summary" ftype="txt" lines_diff="2">
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parents: 0
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205 <assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
iuc
parents: 0
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206 <has_line line="initial heterozygosities = 0.04,0.01"/>
3
460fad600dce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit 0d2b1b7f07cf050b76bb905540f382be7e1cd68f
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parents: 2
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207 <has_text text="Homozygous (aaa) 7.70599% 100%"/>
1
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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parents: 0
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208 </assert_contents>
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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parents: 0
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209 </output>
0
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210 </test>
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211 </tests>
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212 <help><![CDATA[
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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213
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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214 GenomeScope 2.0: Reference-free profiling of polyploid genomes
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215 ==============================================================
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216
1
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parents: 0
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217 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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218 unassembled sequencing data.
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219
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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parents: 0
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220 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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221
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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222 -----
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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223
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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224 .. class:: infomark
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225
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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226 **Topological relationships**
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227
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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228 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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229
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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230 For ploidies of 4 and greater, there are multiple possible topologies. For example, the two tetraploid topologies are:
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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231
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232 ::
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233
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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234 AAAA → AAAB → AABC → ABCD
3169a38c2656 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec"
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235 AAAA → AABB → AABC → ABCD
0
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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236
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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237 ]]></help>
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238 <citations>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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239 <citation type="doi">10.1093/bioinformatics/btx153</citation>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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240 <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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241 </citations>
b2f674562a18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"
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242 </tool>