# HG changeset patch
# User dereeper
# Date 1757683039 0
# Node ID bf77c62428fcb25409f6f57f07f7e5cfeb73d141
# Parent  a7390bf9ac225c4d898ba6a658c8a5125f5b52f8
Uploaded

diff -r a7390bf9ac22 -r bf77c62428fc PanExplorer.xml
--- a/PanExplorer.xml	Tue Sep 09 19:45:06 2025 +0000
+++ b/PanExplorer.xml	Fri Sep 12 13:17:19 2025 +0000
@@ -23,11 +23,12 @@
 touch $vcf;
 touch $vntr_matrix;
 touch $gfa_file;
+touch $coregenes_alignment;
 
 #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 -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >>$logfile 2>&1;
+    snakemake --cores 1 --config identity=$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 $software=="orthofinder"
     snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >>$logfile 2>&1;
 #else if $software=="cactus"
@@ -77,6 +78,7 @@
 	</conditional>
 
   <param name="min_identity" type="text" value="80" label="Minimum percentage identity for BlastP" />
+  <param name="generate_core_genes_alignment" type="boolean" label="Generate an alignment of core-genes" help="This option is active for roary only" />
  </inputs>
 
  <outputs>