# HG changeset patch
# User estrain
# Date 1680283223 14400
# Node ID daa764b0aae8b3fb8621650fcb51090616c5c10f
# Parent  0bb4666ac5ed40098500bf7c34b4708cb9ec6ebc
Uploaded

diff -r 0bb4666ac5ed -r daa764b0aae8 emmtyper/emmtyper.xml
--- a/emmtyper/emmtyper.xml	Fri Mar 31 13:16:20 2023 -0400
+++ b/emmtyper/emmtyper.xml	Fri Mar 31 13:20:23 2023 -0400
@@ -14,53 +14,6 @@
     <help><![CDATA[
         Usage: emmtyper [OPTIONS] [FASTA]...
 
-  Welcome to emmtyper.
-
-  Usage:
-
-  emmtyper *.fasta
-
-Options:
-  --version                       Show the version and exit.
-  -w, --workflow [blast|pcr]      Choose workflow  [default: blast]
-  -d, --blast_db TEXT             Path to EMM BLAST DB
-  -k, --keep                      Keep BLAST and isPcr output files.
-  -d, --cluster-distance INTEGER  Distance between cluster of matches to
-                                  consider as different clusters.  [default:
-                                  500]
-  -o, --output TEXT               Output stream. Path to file for output to a
-                                  file.  [default: stdout]
-  -f, --output-format [short|verbose|visual]
-                                  Output format.
-  --dust [yes|no|level window linker]
-                                  [BLAST] Filter query sequence with DUST.
-                                  [default: no]
-  --percent-identity INTEGER      [BLAST] Minimal percent identity of
-                                  sequence.  [default: 95]
-  --culling-limit INTEGER         [BLAST] Total hits to return in a position.
-                                  [default: 5]
-  --mismatch INTEGER              [BLAST] Threshold for number of mismatch to
-                                  allow in BLAST hit.  [default: 4]
-  --align-diff INTEGER            [BLAST] Threshold for difference between
-                                  alignment length and subject length in BLAST
-                                  hit.  [default: 5]
-  --gap INTEGER                   [BLAST] Threshold gap to allow in BLAST hit.
-                                  [default: 2]
-  --blast-path TEXT               [BLAST] Specify full path to blastn
-                                  executable.
-  --primer-db TEXT                [isPcr] PCR primer. Text file with 3
-                                  columns: Name, Forward Primer, Reverse
-                                  Primer. 
-  --min-perfect INTEGER           [isPcr] Minimum size of perfect match at 3'
-                                  primer end.  [default: 15]
-  --min-good INTEGER              [isPcr] Minimum size where there must be 2
-                                  matches for each mismatch.  [default: 15]
-  --max-size INTEGER              [isPcr] Maximum size of PCR product.
-                                  [default: 2000]
-  --ispcr-path TEXT               [isPcr] Specify full path to isPcr
-                                  executable.
-  --help                          Show this message and exit.
-
     ]]></help>
     <citations>
         <citation type="bibtex">