# HG changeset patch
# User dereeper
# Date 1757693684 0
# Node ID 963038acf99998c857eaeb4c2fb5e1460d9cc5bc
# Parent  bf77c62428fcb25409f6f57f07f7e5cfeb73d141
Uploaded

diff -r bf77c62428fc -r 963038acf999 PanExplorer.xml
--- 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>