Mercurial > repos > iuc > ppanggolin_rarefaction

annotate ppanggolin_rarefaction.xml @ 2:e717755c87aa draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin commit 29098ae57dcc42db8f9adf321d31ed37fb999d17
author iuc
date Mon, 24 Nov 2025 12:55:45 +0000
parents 8d43b1705153
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8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
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1 <tool id="ppanggolin_rarefaction" name="PPanGGOLiN rarefaction" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
iuc
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2 <description>computes the rarefaction curve of the pangenome</description>
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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3 <macros>
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iuc
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4 <import>macros.xml</import>
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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5 </macros>
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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6 <expand macro="xrefs"/>
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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7 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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10 mkdir -p ./tmp_ppanggolin/rarefaction &&
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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11 mkdir -p ./tmp_ppanggolin/tmpdir_rarefaction &&
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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13 ppanggolin rarefaction
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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14 --pangenome '$pangenome_h5'
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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15 --output ./tmp_ppanggolin/rarefaction
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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16 --tmpdir ./tmp_ppanggolin/tmpdir_rarefaction
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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17 --force
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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18 --cpu "\${GALAXY_SLOTS:-4}"
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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19 --disable_prog_bar
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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21 --depth $depth
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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22 --min $min
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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23 --max $max
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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25 #if str($nb_of_partitions) != "":
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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26 --nb_of_partitions $nb_of_partitions
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27 #end if
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29 #if "output_rarefaction_csv" in $advanced_pangenome_optional_files:
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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30 && cat ./tmp_ppanggolin/rarefaction/rarefaction.csv > '${rarefaction_csv}'
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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31 #end if
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32 #if "output_rarefaction_parameters_csv" in $advanced_pangenome_optional_files:
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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33 && cat ./tmp_ppanggolin/rarefaction/rarefaction_parameters.csv > '${rarefaction_parameters_csv}'
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34 #end if
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35 && cat ./tmp_ppanggolin/rarefaction/rarefaction_curve.html > '${rarefaction_curve_html}'
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37 ]]></command>
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39 <inputs>
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41 <expand macro="inputs_pangenome"/>
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43 <param argument="--depth" type="integer" value="30" min="1" max="100" label="The number of sampling for each genome" help="Default=30 ; min=1 ; max=100. Warning: if this value is greater than 30, the computation will be VERY intensive and it will take a long time.">
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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44 </param>
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46 <param argument="--min" type="integer" value="1" min="1" max="499" label="The minimal number of genomes in a sample" help="Default=1 ; min=1 ; max=499. The min value must be lower than the max value.">
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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47 </param>
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49 <param argument="--max" type="integer" value="100" min="1" max="500" label="The maximal number of genomes in a sample" help="Default=1 ; min=1 ; max=500. The min value must be lower than the max value. Warning: if if this value is greater than 100, the computation will be VERY intensive and it will take a long time.">
8d43b1705153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
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50 </param>
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52 <expand macro="inputs_nb_of_partitions"/>
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53
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54 <param name="advanced_pangenome_optional_files" type="select" label="Add the following output files in the Galaxy history" multiple="true" optional="true" display="checkboxes" >
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55 <option value="output_rarefaction_csv" selected="true">Rarefaction data in tabular format (csv)</option>
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56 <option value="output_rarefaction_parameters_csv" selected="true">Rarefaction parameters in tabular format (csv)</option>
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57 </param>
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59 </inputs>
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61 <outputs>
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63 <data name="rarefaction_csv" format="csv" label="PPanGGOLiN rarefaction on ${on_string}: Rarefaction data (csv)" >
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64 <filter>advanced_pangenome_optional_files and "output_rarefaction_csv" in advanced_pangenome_optional_files</filter>
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65 </data>
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66 <data name="rarefaction_parameters_csv" format="csv" label="PPanGGOLiN rarefaction on ${on_string}: Rarefaction parameters (csv)" >
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67 <filter>advanced_pangenome_optional_files and "output_rarefaction_parameters_csv" in advanced_pangenome_optional_files</filter>
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68 </data>
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70 <data name="rarefaction_curve_html" format="html" label="PPanGGOLiN rarefaction on ${on_string}: Rarefaction curve" />
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72 </outputs>
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74 <tests>
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75 <test expect_num_outputs="3">
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76 <param name="pangenome_h5" value="h5/test_data.h5" ftype="h5"/>
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77 <param name="depth" value="30"/>
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78 <param name="min" value="1"/>
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79 <param name="max" value="100"/>
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80 <output name="rarefaction_csv" >
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81 <assert_contents>
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82 <has_size value="4045" delta="100"/>
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83 </assert_contents>
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84 </output>
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85 <output name="rarefaction_parameters_csv" >
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86 <assert_contents>
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87 <has_size value="324" delta="50"/>
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88 </assert_contents>
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89 </output>
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90 <output name="rarefaction_curve_html" >
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91 <assert_contents>
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92 <has_size value="4575692" delta="100"/>
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93 </assert_contents>
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94 </output>
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95 </test>
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96 </tests>
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97
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98 <help><![CDATA[
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99
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100 PPanGGOLiN_ (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either assembled
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101 genomic DNA sequences or provided genome annotations. PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene
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102 families in persistent, shell and cloud genomes. It integrates both information on protein-coding genes and their genomic neighborhood to build a graph
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103 of gene families where each node is a gene family, and each edge is a relation of genetic contiguity.
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104
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105 The `ppanggolin rarefaction` command generates a rarefaction curve. It represents the evolution of the number of gene families for each partition as you add more genomes to the pangenome. It has been used a lot in the literature as an indicator of the diversity that you are missing with your dataset on your taxonomic group (Tettelin et al., 2005). The idea is that if at some point when you keep adding genomes to your pangenome you do not add any more gene families, you might have access to your entire taxonomic group’s diversity. On the contrary, if you are still adding a lot of genes you may be still missing a lot of gene families.
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106
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107 There are 8 partitions represented. For each of the partitions, there are multiple representations of the observed data. You can find the observed means, medians, 1st and 3rd quartiles of the number of gene families per number of genome used. You can also find the best fitting of the data by the Heaps’ law, which is usually used to represent this evolution of the diversity in terms of gene families in each of the partitions.
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108
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109 .. _PPanGGOLiN: https://github.com/labgem/PPanGGOLiN
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110 .. _documentation: https://ppanggolin.readthedocs.io/en/latest/user/PangenomeAnalyses/pangenomeAnalyses.html#rarefaction-curve
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111
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112 ]]></help>
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113
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114 <expand macro="citation"/>
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115
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116 </tool>
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117