Mercurial > repos > dereeper > pangenome_explorer

changeset 24:bf77c62428fc draft

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Uploaded
author dereeper
date Fri, 12 Sep 2025 13:17:19 +0000
parents a7390bf9ac22
children 963038acf999
files PanExplorer.xml
diffstat 1 files changed, 3 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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>