Merge pull request #301 from andrewjpage/iterative_cdhit_text

update usage text for iterative CD-hit
sanger-pathogens · Jan 16, 2017 · 96d1d16 · 96d1d16
2 parents 4a5c3e4 + 2b58658
commit 96d1d16
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diff --git a/dist.ini b/dist.ini
@@ -1,5 +1,5 @@
 name    = Bio-Roary
-version = 3.7.0
+version = 3.7.1
 author  = Andrew J. Page <[email protected]>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute

diff --git a/lib/Bio/Roary/CommandLine/IterativeCdhit.pm b/lib/Bio/Roary/CommandLine/IterativeCdhit.pm
@@ -97,10 +97,12 @@ sub usage_text {
 
     return <<USAGE;
 Usage: iterative_cdhit [options]
-Iteratively cluster a set of proteins with CD-hit, lower the threshold each time and extracting core genes (1 per isolate) to another file, and remove them from the input proteins file.
+Iteratively cluster a FASTA file of proteins with CD-hit, lower the threshold each time and extracting core genes (1 per isolate) to another file, and remove them from the input proteins file.
+
+Required arguments:
+         -m STR   input FASTA file of protein sequences [_combined_files]
 
 Options: -p INT   number of threads [1]
-         -m STR   output filename for combined proteins [_combined_files]
          -n INT   number of isolates [1]
          -c STR   cd-hit output filename [_clustered]
          -f STR   output filename for filtered sequences [_clustered_filtered.fa]