fix usage

sanger-pathogens · Aug 22, 2017 · 8d34a81 · 8d34a81
1 parent f631079
commit 8d34a81
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/lib/Bio/Roary/CommandLine/Roary.pm b/lib/Bio/Roary/CommandLine/Roary.pm
@@ -346,12 +346,12 @@ Options: -p INT    number of threads [1]
          -r        create R plots, requires R and ggplot2
          -s        dont split paralogs
          -t INT    translation table [11]
-		 -ap       allow paralogs in core alignment
+         -ap       allow paralogs in core alignment
          -z        dont delete intermediate files
          -v        verbose output to STDOUT
          -w        print version and exit
          -y        add gene inference information to spreadsheet, doesnt work with -e
-	 -iv STR   Change the MCL inflation value [1.5]
+         -iv STR   Change the MCL inflation value [1.5]
          -h        this help message
 
 Example: Quickly generate a core gene alignment using 8 threads

diff --git a/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm b/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm
@@ -134,7 +134,7 @@ Options: -o STR    output filename [core_gene_alignment.aln]
          -cd FLOAT percentage of isolates a gene must be in to be core [99]
          -m STR    directory containing gene multi-FASTAs [pan_genome_sequences]
          -s STR    gene presence and absence spreadsheet [gene_presence_absence.csv]
-		 -p        allow paralogs
+         -p        allow paralogs
          -z        dont delete intermediate files
          -v        verbose output to STDOUT
          -h        this help message