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1 <tool id="pangenome_explorer" name="PanExplorer2" version="2.0">
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2 <description> Bacterial pan-genome analysis </description>
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3 <requirements>
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7
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4 <requirement type="package" version="1.30">perl-yaml</requirement>
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5 <requirement type="package" version="3.8.7">singularity</requirement>
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18
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6 <container type="docker">docker.io/dereeper/panexplorer_workflow:latest</container>
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2
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7 </requirements>
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8
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9 <command><![CDATA[
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7
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10
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11 export PANEX_PATH=/usr/local/bin/PanExplorer_workflow;
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14
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12
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13 #if str($mode.mode) == "accessions":
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14 perl ${__tool_directory__}/generateConfig.pl 'None' '$input' config.yaml 'None';
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15 #else if str($mode.mode) == "genbanks":
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16 perl ${__tool_directory__}/generateConfig.pl '$private_genomes' 'None' config.yaml 'None';
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17 #else if str($mode.mode) == "fasta":
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18 perl ${__tool_directory__}/generateConfig.pl '$private_genomes' 'None' config.yaml '$private_genomes_fasta';
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19 #end if
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20
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21 cat config.yaml >$logfile;
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22
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23 touch $vcf;
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24
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25 #if $software=="pgap"
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26 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >>$logfile 2>&1;
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27 #else if $software=="roary"
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28 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >>$logfile 2>&1;
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29 #else if $software=="orthofinder"
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30 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >>$logfile 2>&1;
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31 #else if $software=="cactus"
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32 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 >>$logfile 2>&1;
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33 #else if $software=="pggb"
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34 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG >>$logfile 2>&1;
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35 #else
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36 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG >>$logfile 2>&1;
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37 #end if
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38
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2
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39
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40 ]]></command>
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41
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42
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43 <inputs>
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44 <conditional name="mode">
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45 <param name = "mode" type="select" label="What is your inputs?">
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46 <option value="accessions">Prokaryote genomes: List of Genbank assembly accessions (GCA)</option>
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47 <option value="genbanks">Prokaryote genomes: Genbank files</option>
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48 <option value="fasta">Eukaryote genomes: FASTA + GFF files</option>
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49 </param>
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50 <when value="accessions">
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51 <param name="input" type="text" multiple="true" label="List of genbank identifiers" help="Coma separated list (ex: GCA_000007385.1,GCA_000010025.1,GCA_000019585.2)"/>
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52 <param type="select" name="software" label="Choose the pan-genome software">
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53 <option value="roary">Roary</option>
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54 <option value="panacota">PanACoTA</option>
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55 <option value="pggb">PanGenome Graph Builder (PGGB)</option>
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56 </param>
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57 </when>
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58 <when value="genbanks">
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59 <param name="private_genomes" type="data" format="zip" label="Zip of genbank files" optional="true"/>
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60 <param type="select" name="software" label="Choose the pan-genome software">
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61 <option value="roary">Roary</option>
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62 <option value="panacota">PanACoTA</option>
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63 <option value="pggb">PanGenome Graph Builder (PGGB)</option>
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64 </param>
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65 </when>
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66 <when value="fasta">
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67 <param name="private_genomes_fasta" type="data" format="zip" label="Zip of Fasta files" optional="true"/>
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68 <param name="private_genomes" type="data" format="zip" label="Zip of GFF files" optional="true"/>
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69 <param type="select" name="software" label="Choose the pan-genome software">
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70 <option value="orthofinder">OrthoFinder</option>
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71 <option value="cactus">Minigraph-Cactus</option>
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72 <option value="pggb">PanGenome Graph Builder (PGGB)</option>
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73 </param>
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74 </when>
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75 </conditional>
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76
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77 <param name="min_identity" type="text" value="80" label="Minimum percentage identity for BlastP" />
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78 </inputs>
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79
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80 <outputs>
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81 <data from_work_dir="outputs/pav_matrix.tsv" format="txt" name="output" label="Pangenome presence absence matrix"/>
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82 <data from_work_dir="outputs/heatmap.svg.complete.pdf.distance_matrix.hclust.newick" format="newick" name="njtree" label="PanBased NJ tree"/>
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83 <data from_work_dir="outputs/genomes/genes.txt" format="txt" name="genes" label="Genes"/>
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84 <data from_work_dir="outputs/cog_output.txt" format="txt" name="cogfile" label="COG assignation"/>
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85 <data from_work_dir="outputs/GCskew.txt" format="txt" name="gcfile" label="GC_percent"/>
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86 <data from_work_dir="outputs/upsetr.svg" format="svg" name="upset" label="Upset Diagram"/>
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87 <data from_work_dir="outputs/heatmap.svg.gz" format="svg" name="heatmap" label="Presence Absence Heatmap"/>
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88 <data from_work_dir="outputs/heatmap.svg.heatmap_plotly.html" format="html" name="heatmap_html" label="Presence Absence Heatmap interactive"/>
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89 <data from_work_dir="outputs/cog_stats.txt" format="tabular" name="outcog_stat" label="COG category counts"/>
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90 <data from_work_dir="outputs/cog_stats2.txt" format="tabular" name="outcog_stat2" label="COG category 2 counts"/>
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91 <data from_work_dir="outputs/cog_of_clusters.txt" format="tabular" name="outcog_clusters" label="COG of clusters"/>
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92 <data from_work_dir="outputs/fastani.out.matrix.complete" format="tabular" name="fastani" label="ANI" />
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93 <data from_work_dir="outputs/fastani.out.svg" format="svg" name="ani_svg" label="ANI heatmap" />
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94 <data from_work_dir="outputs/rarefaction_curves.txt" format="txt" name="rarefaction_curves" label="Rarefaction curves data"/>
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95 <data from_work_dir="outputs/rarefaction_curves.svg" format="svg" name="rarefaction_curves_svg" label="Rarefaction curves"/>
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96 <data from_work_dir="outputs/heaps.tsv" format="txt" name="heaps" label="Heaps law alpha"/>
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97 <data from_work_dir="outputs/heatmap.svg.complete.pdf.distance_matrix.txt" format="txt" name="distance_matrix" label="Accessory based distance matrix"/>
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98 <data from_work_dir="outputs/all_genomes.vcf" format="vcf" name="vcf" label="VCF file"/>
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99 <data format="txt" name="logfile" label="Logfile"/>
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100 <data format="txt" name="roary_log" label="Roary Logfile"/>
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101 </outputs>
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102 <tests>
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103 <test>
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104 <param name="input" value="GCA_000007385.1,GCA_000010025.1,GCA_000019585.2"/>
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105 <param name="min_identity" value="80"/>
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106 <param name="software" value="panacota"/>
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107 <param name="private_genomes" value=""/>
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108 <param name="private_genomes_fasta" value=""/>
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109 <output name="distance_matrix" value="Accessory_based_distance_matrix.txt"/>
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110 <output name="fastani" value="ANI.txt"/>
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111 </test>
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112 </tests>
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113 <help>
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114
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115 PanExplorer
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116 =======
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117
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118 PanExplorer workflow is a snakemake worklow that can be run in the backend of the PanExplorer web application.
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119
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120 Homepage: https://panexplorer.southgreen.fr/
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121
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122 It allows to perform a pan-genome analysis using published and annotated bacteria genomes, using different tools that can be invoked: Roary, PGAP, PanACoTA.
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123
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124 Pangenome graph builder softwares have been implemented recently in the pipeline: Minigraph-Cactus and PGGB (PanGenome Graph Builder)
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125
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126 It provides a presence/absence matrix of genes, an UpsetR Diagram for synthetizing the matrix information and a COG assignation summary for each strain.
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127
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128 Please visit the GitHub page for the PanExplorer workflow at: https://github.com/SouthGreenPlatform/PanExplorer_workflow
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129
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130
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131 Inputs
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132 ------
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133
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134 Inputs can be provided as one of the following:
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135
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136 * **List of genbank assembly identifiers** comma-separated(ex: GCA_000007385.1,GCA_000010025.1,GCA_000019585.2)
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137 * **Zip of genbank files** They must include the gene annotation and the complete sequence data
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138 * **Zip of FASTA file of genomes + Zip of GFF annotation files**: In order to make the association between sequence and annotation, they must be named with the same basename as follows: genome1.fasta, genome1.gff, myspeciesXXX.fasta, myspeciesXXX.gff...
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139
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140
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141
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142 Outputs
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143 ------
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144
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145 Among the outputs:
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146
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147 * **Pangenome presence absence matrix** Pangene presence/absence matrix indicating the PAV (Presence Absence Variation) of clustered genes.
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148 * **PanBased NJ tree** Distance tree based on PAV data
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149 * **Heaps law alpha** Estimating if a pan-genome is open or closed based on a Heaps law model.
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150 * **Rarefaction curves** A rarefaction curve is the cumulative number of gene clusters we observe as more and more genomes are being considered
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151 * **ANI** Average Nucleotide Identity between genomes
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152 * **ANI heatmap** image as SVG
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153 * **VCF file** If a pan-genome graph software has been selected, it provides a VCF of variations among all samples.
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154
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155
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156
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157 </help>
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158 <citations>
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159 <citation type="doi">10.1093/bioinformatics/btac504</citation>
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160 </citations>
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161
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162 </tool>
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