Mercurial > repos > dereeper > pangenome_explorer
changeset 25:963038acf999 draft default tip
Uploaded
| author | dereeper |
|---|---|
| date | Fri, 12 Sep 2025 16:14:44 +0000 |
| parents | bf77c62428fc |
| children | |
| files | PanExplorer.xml |
| diffstat | 1 files changed, 5 insertions(+), 1 deletions(-) [+] |
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--- a/PanExplorer.xml Fri Sep 12 13:17:19 2025 +0000 +++ b/PanExplorer.xml Fri Sep 12 16:14:44 2025 +0000 @@ -28,7 +28,10 @@ #if $software=="pgap" snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >>$logfile 2>&1; #else if $software=="roary" - snakemake --cores 1 --config identity=$min_identity generate_core_genes_alignment=$generate_core_genes_alignment -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >>$logfile 2>&1; +#else if $software=="roary" and $generate_core_genes_alignment=="true" + snakemake --cores 1 --config identity=$min_identity generate_core_genes_alignment=True -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >>$logfile 2>&1; +#else if $software=="roary" + snakemake --cores 1 --config identity=$min_identity generate_core_genes_alignment=False -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >>$logfile 2>&1; #else if $software=="orthofinder" snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >>$logfile 2>&1; #else if $software=="cactus" @@ -101,6 +104,7 @@ <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 from_work_dir="outputs/pggb_out/all_genomes.fa.smooth.final.gfa" format="gfa1" name="gfa_file" label="GFA file"/> + <data from_work_dir="outputs/roary_outdir/core_gene_alignment.aln" format="fasta" name="coregenes_alignment" label="Coregenes FASTA alignment"/> <data format="txt" name="logfile" label="Logfile"/> <data format="txt" name="roary_log" label="Roary Logfile"/> </outputs>