Mercurial > repos > dereeper > pangenome_explorer
changeset 19:b8ea3d2945b5 draft
Uploaded
| author | dereeper |
|---|---|
| date | Mon, 27 Jan 2025 13:02:48 +0000 |
| parents | 716821f47909 |
| children | e23149f1f55c |
| files | PanExplorer.xml |
| diffstat | 1 files changed, 26 insertions(+), 65 deletions(-) [+] |
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--- a/PanExplorer.xml Tue Dec 17 13:19:43 2024 +0000 +++ b/PanExplorer.xml Mon Jan 27 13:02:48 2025 +0000 @@ -1,13 +1,6 @@ <tool id="pangenome_explorer" name="PanExplorer2" version="2.0"> <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> <container type="docker">docker.io/dereeper/panexplorer_workflow:latest</container> @@ -27,55 +20,23 @@ cat config.yaml >$logfile; -if [ ! -f ${__tool_directory__}/panexplorer_workflow_latest.sif ]; then wget -O ${__tool_directory__}/panexplorer_workflow_latest.sif https://panexplorer.southgreen.fr/singularity/panexplorer_workflow_latest.sif >>$logfile 2>&1;fi; - - - - +touch $vcf; #if $software=="pgap" -singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG 1>snakefile 2>>$logfile; + snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >>$logfile 2>&1; #else if $software=="roary" -singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG 1>snakefile 2>>$logfile; + snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >>$logfile 2>&1; #else if $software=="orthofinder" -singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset 1>snakefile 2>>$logfile; + snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >>$logfile 2>&1; #else if $software=="cactus" - singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 1>snakefile 2>>$logfile; + snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 >>$logfile 2>&1; #else if $software=="pggb" -singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG 1>snakefile 2>>$logfile; + snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG >>$logfile 2>&1; #else - singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG 1>snakefile 2>>$logfile; + snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG >>$logfile 2>&1; #end if - -singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif snakemake --cores 1 --config identity=$min_identity -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> @@ -117,24 +78,24 @@ </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 from_work_dir="outputs/pav_matrix.tsv" format="txt" name="output" label="Pangenome presence absence matrix"/> + <data from_work_dir="outputs/heatmap.svg.complete.pdf.distance_matrix.hclust.newick" format="newick" name="njtree" label="PanBased NJ tree"/> + <data from_work_dir="outputs/genomes/genes.txt" format="txt" name="genes" label="Genes"/> + <data from_work_dir="outputs/cog_output.txt" format="txt" name="cogfile" label="COG assignation"/> + <data from_work_dir="outputs/GCskew.txt" format="txt" name="gcfile" label="GC_percent"/> + <data from_work_dir="outputs/upsetr.svg" format="svg" name="upset" label="Upset Diagram"/> + <data from_work_dir="outputs/heatmap.svg.gz" format="svg" name="heatmap" label="Presence Absence Heatmap"/> + <data from_work_dir="outputs/heatmap.svg.heatmap_plotly.html" format="html" name="heatmap_html" label="Presence Absence Heatmap interactive"/> + <data from_work_dir="outputs/cog_stats.txt" format="tabular" name="outcog_stat" label="COG category counts"/> + <data from_work_dir="outputs/cog_stats2.txt" format="tabular" name="outcog_stat2" label="COG category 2 counts"/> + <data from_work_dir="outputs/cog_of_clusters.txt" format="tabular" name="outcog_clusters" label="COG of clusters"/> + <data from_work_dir="outputs/fastani.out.matrix.complete" format="tabular" name="fastani" label="ANI" /> + <data from_work_dir="outputs/fastani.out.svg" format="svg" name="ani_svg" label="ANI heatmap" /> + <data from_work_dir="outputs/rarefaction_curves.txt" format="txt" name="rarefaction_curves" label="Rarefaction curves data"/> + <data from_work_dir="outputs/rarefaction_curves.svg" format="svg" name="rarefaction_curves_svg" label="Rarefaction curves"/> + <data from_work_dir="outputs/heaps.tsv" format="txt" name="heaps" label="Heaps law alpha"/> + <data from_work_dir="outputs/heatmap.svg.complete.pdf.distance_matrix.txt" format="txt" name="distance_matrix" label="Accessory based distance matrix"/> + <data from_work_dir="outputs/all_genomes.vcf" format="vcf" name="vcf" label="VCF file"/> <data format="txt" name="logfile" label="Logfile"/> <data format="txt" name="roary_log" label="Roary Logfile"/> </outputs>