| Previous changeset 0:b2f674562a18 (2021-04-30) Next changeset 2:01210c4e9144 (2022-08-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit a0ba4e5bb9dd542bbf1395af64e59b9f72823fec" |
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modified:
genomescope.xml test-data/genomescope-out1-2.txt |
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| diff -r b2f674562a18 -r 3169a38c2656 genomescope.xml --- a/genomescope.xml Fri Apr 30 20:21:25 2021 +0000 +++ b/genomescope.xml Sat Jun 26 14:17:47 2021 +0000 |
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| b'@@ -1,7 +1,8 @@\n-<tool id="genomescope" name="GenomeScope" version="@VERSION@" profile="20.01">\n- <description>Analyze unassembled short reads</description>\n+<tool id="genomescope" name="GenomeScope" version="@VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">\n+ <description>reference-free genome profiling</description>\n <macros>\n <token name="@VERSION@">2.0</token>\n+ <token name="@SUFFIX_VERSION@">1</token>\n </macros>\n <requirements>\n <requirement type="package" version="@VERSION@">genomescope2</requirement>\n@@ -12,7 +13,9 @@\n --input \'$input\'\n --output .\n --kmer_length $kmer_length \n- $no_unique_sequence $testing $trace_flag\n+ $output_options.no_unique_sequence \n+ $advanced_options.testing \n+ $advanced_options.trace_flag\n #if $ploidy:\n --ploidy $ploidy\n #end if\n@@ -22,44 +25,60 @@\n #if $max_kmercov:\n --max_kmercov $max_kmercov\n #end if\n- #if $topology:\n- --topology $topology\n+ #if $advanced_options.topology:\n+ --topology $advanced_options.topology\n #end if\n- #if $initial_repetitiveness:\n- --initial_repetitiveness $initial_repetitiveness\n+ #if $advanced_options.initial_repetitiveness:\n+ --initial_repetitiveness $advanced_options.initial_repetitiveness\n #end if\n- #if $initial_heterozygosities:\n- --initial_heterozygosities $initial_heterozygosities\n+ #if $advanced_options.initial_heterozygosities:\n+ --initial_heterozygosities \'${advanced_options.initial_heterozygosities}\'\n #end if\n- #if $transform_exp:\n- --transform_exp $transform_exp\n+ #if $advanced_options.transform_exp:\n+ --transform_exp $advanced_options.transform_exp\n #end if\n- #if $true_params:\n- --true_params $true_params\n+ #if $advanced_options.true_params:\n+ --true_params \'${advanced_options.true_params}\'\n #end if\n- #if $num_rounds:\n- --num_rounds $num_rounds\n+ #if $advanced_options.num_rounds:\n+ --num_rounds $advanced_options.num_rounds\n #end if\n ]]>\n </command>\n <inputs>\n <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."/>\n- <param name="model_output" type="boolean" label="Add the model parameters to your history"/>\n- <param name="summary_output" type="boolean" label="Output a summary of the analysis"/>\n- <param name="progress_output" type="boolean" label="Additional information for each optimization round"/>\n- <param argument="--ploidy" type="integer" optional="true" label="Ploidy for model to use" help="Default: 2"/>\n+ <param argument="--ploidy" type="integer" min="1" max="6" optional="true" label="Ploidy for model to use" help="Default: 2"/>\n <param argument="--kmer_length" type="integer" value="21" optional="false" label="K-mer length used to calculate k-mer spectra"/>\n- <param argument="--lambda" type="integer" optional="true" label="Optional initial kmercov estimate for model to use"/>\n- <param argument="--max_kmercov" type="integer" optional="true" label="Optional maximum k-mer coverage threshold" help="K-mers with coverage greater than max_kmercov are ignored by the model"/>\n- <param argument="--no_unique_sequence" type="boolean" truevalue="--no_unique_sequence" falsevalue="" label="Turn off yellow unique sequence line in plots"/>\n- <param argument="--topology" type="integer" optional="true" label="Flag for topology for model to use"/>\n- <param arg'..b'tion>\n+ <section name="output_options">\n+ <param name="output_files" value="summary_output"/>\n+ </section>\n+ <output name="linear_plot" ftype="png">\n+ <assert_contents>\n+ <has_size value="213366" delta="300"/>\n+ </assert_contents>\n+ </output>\n+ <output name="log_plot" ftype="png">\n+ <assert_contents>\n+ <has_size value="218425" delta="300"/>\n+ </assert_contents>\n+ </output>\n+ <output name="transformed_linear_plot" ftype="png">\n+ <assert_contents>\n+ <has_size value="217280" delta="300"/>\n+ </assert_contents>\n+ </output>\n+ <output name="transformed_log_plot" ftype="png">\n+ <assert_contents>\n+ <has_size value="229021" delta="300"/>\n+ </assert_contents>\n+ </output>\n+ <output name="summary" ftype="txt" lines_diff="2">\n+ <assert_contents>\n+ <has_line line="initial heterozygosities = 0.04,0.01"/>\n+ <has_text text="Homozygous (aaa) 6.03606% 100%"/>\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n <help><![CDATA[\n@@ -102,18 +198,25 @@\n GenomeScope 2.0: Reference-free profiling of polyploid genomes\n ==============================================================\n \n-GenomeScope 2.0 applies classical insights from combinatorial theory to establish\n-a detailed mathematical model of how k-mer frequencies will be distributed in\n-heterozygous and polyploid genomes. GenomeScope 2.0 employs a polyploid-aware\n-mixture model that, within seconds, accurately infers genome properties from\n-unassembled sequencing data. GenomeScope 2.0 uses the k-mer count distribution,\n-e.g. from KMC or Jellyfish, and produces a report and several informative plots\n-describing the genome properties. We validate the approach on simulated polyploid\n-data created using a generative model with parameters for genome size, heterozygosity,\n-repetitiveness, ploidy, and sequencing coverage, and find GenomeScope 2.0 retains\n-accuracy across a broad range of realistic and extreme parameter values. We also\n-validate GenomeScope 2.0 by analyzing genuine sequence data from 11 diverse\n-polyploid genomes with known genome characteristics.\n+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\n+unassembled sequencing data. \n+\n+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.\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Topological relationships**\n+\n+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.\n+\n+For ploidies of 4 and greater, there are multiple possible topologies. For example, the two tetraploid topologies are:\n+\n+ ::\n+\n+ AAAA \xe2\x86\x92 AAAB \xe2\x86\x92 AABC \xe2\x86\x92 ABCD\n+ AAAA \xe2\x86\x92 AABB \xe2\x86\x92 AABC \xe2\x86\x92 ABCD\n \n ]]></help>\n <citations>\n' |
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| diff -r b2f674562a18 -r 3169a38c2656 test-data/genomescope-out1-2.txt --- a/test-data/genomescope-out1-2.txt Fri Apr 30 20:21:25 2021 +0000 +++ b/test-data/genomescope-out1-2.txt Sat Jun 26 14:17:47 2021 +0000 |
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| @@ -1,5 +1,5 @@ GenomeScope version 2.0 -input file = /tmp/tmp32yh4464/files/1/e/2/dataset_1e2ac011-2bc8-45cf-971a-75abc3cda6d6.dat +input file = /tmp/tmpiqlcd57_/files/3/b/b/dataset_3bb1f7de-024a-4b3c-aa68-e735f06791c1.dat output directory = . p = 2 k = 21 |