Mercurial > repos > dereeper > pangenome_explorer
view PanExplorer.xml @ 9:24676ef2945d draft
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author | dereeper |
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date | Thu, 30 May 2024 16:18:04 +0000 |
parents | f919ffe96425 |
children | d103c41b6931 |
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<tool id="PanExplorer" name="PanExplorer" version="1.0"> <description> Bacterial pan-genome analysis </description> <requirements> <!-- <requirement type="package" version="2.2.26">blast-legacy</requirement> <requirement type="package" version="7.480">mafft</requirement> <requirement type="package" version="14.137">mcl</requirement> <requirement type="package" version="3.697">phylip</requirement> <requirement type="package" version="1.7.2">perl-bioperl</requirement> --> <requirement type="package" version="1.30">perl-yaml</requirement> <requirement type="package" version="3.8.7">singularity</requirement> </requirements> <command><![CDATA[ export PANEX_PATH=${__tool_directory__}; perl ${__tool_directory__}/Perl/generateConfig.pl '$private_genomes' '$input' config.yaml '$private_genomes_fasta'; cat config.yaml >$logfile; wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1; #if $software=="pgap" sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile; #else if $software=="roary" sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >snakefile; #else if $software=="orthofinder" sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >snakefile; #else if $software=="cactus" cp -rf \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 snakefile; #else if $software=="pggb" sed "s/identity\=30/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG >snakefile; #else sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG >snakefile; #end if singularity exec \$PANEX_PATH/panexplorer.sif snakemake --cores 1 -s snakefile >>$logfile 2>&1; cp -rf outputs/upsetr.svg $upset; cp -rf outputs/pav_matrix.tsv $output; cp -rf outputs/heatmap.svg.gz $heatmap; cp -rf outputs/heatmap.svg.heatmap_plotly.html $heatmap_html; cp -rf outputs/rarefaction_curves.txt $rarefaction_curves; cp -rf outputs/rarefaction_curves.svg $rarefaction_curves_svg; cp -rf outputs/heaps.tsv $heaps; cp -rf outputs/heatmap.svg.complete.pdf.distance_matrix.txt $distance_matrix; cp -rf outputs/heatmap.svg.complete.pdf.distance_matrix.hclust.newick $njtree; #if $software!="orthofinder" cp -rf outputs/GCskew.txt $gcfile; cp -rf outputs/cog_output.txt $cogfile; cp -rf outputs/cog_stats.txt $outcog_stat; cp -rf outputs/cog_stats2.txt $outcog_stat2; cp -rf outputs/cog_of_clusters.txt $outcog_clusters; cp -rf outputs/genomes/genes.txt $genes; cp -rf outputs/fastani.out.matrix.complete $fastani; cp -rf outputs/fastani.out.svg $ani_svg; #end if #if $software=="pggb" cp -rf outputs/all_genomes.vcf $vcf; #else touch $vcf; #end if ]]></command> <inputs> <param name="input" type="text" multiple="true" label="List of genbank identifiers" help="Coma separated list (ex: CP000235.1,CP001079.1,CP001759.1,CP015994.2)"/> <param name="private_genomes" type="data" format="zip" label="Zip of genbank or GFF files" optional="true"/> <param name="private_genomes_fasta" type="data" format="zip" label="Zip of Fasta files" optional="true"/> <param name="min_identity" type="text" value="80" label="Minimum percentage identity for BlastP" /> <param type="select" name="software" label="Choose the pan-genome software"> <option value="pgap">PGAP</option> <option value="roary">Roary</option> <option value="panacota">PanACoTA</option> <option value="orthofinder">OrthoFinder</option> <option value="cactus">Minigraph-Cactus</option> <option value="pggb">PanGenome Graph Builder (PGGB)</option> </param> </inputs> <outputs> <data format="txt" name="output" label="Pangenome presence absence matrix"/> <data format="newick" name="njtree" label="PanBased NJ tree"/> <data format="txt" name="genes" label="Genes"/> <data format="txt" name="cogfile" label="COG assignation"/> <data format="txt" name="gcfile" label="GC_percent"/> <data format="svg" name="upset" label="Upset Diagram"/> <data format="svg" name="heatmap" label="Presence Absence Heatmap"/> <data format="html" name="heatmap_html" label="Presence Absence Heatmap interactive"/> <data format="tabular" name="outcog_stat" label="COG category counts"/> <data format="tabular" name="outcog_stat2" label="COG category 2 counts"/> <data format="tabular" name="outcog_clusters" label="COG of clusters"/> <data format="tabular" name="fastani" label="ANI" /> <data format="svg" name="ani_svg" label="ANI heatmap" /> <data format="txt" name="rarefaction_curves" label="Rarefaction curves data"/> <data format="svg" name="rarefaction_curves_svg" label="Rarefaction curves"/> <data format="txt" name="heaps" label="Heaps law alpha"/> <data format="txt" name="distance_matrix" label="Accessory based distance matrix"/> <data format="vcf" name="vcf" label="VCF file"/> <data format="txt" name="logfile" label="Logfile"/> <data format="txt" name="roary_log" label="Roary Logfile"/> </outputs> </tool>