# HG changeset patch
# User dfornika
# Date 1507330191 14400
# Node ID 5d53288c94e6ebd9ed0f10d6f324d97a121cad25
# Parent  d49c55382054d45036d6e85a116bcf5c1730f8ab
planemo upload for repository https://github.com/dfornika/tools-pathogist/tree/master/tools

diff -r d49c55382054 -r 5d53288c94e6 tools/mentalist_call/mentalist_call.xml
--- a/tools/mentalist_call/mentalist_call.xml	Fri Oct 06 18:02:14 2017 -0400
+++ b/tools/mentalist_call/mentalist_call.xml	Fri Oct 06 18:49:51 2017 -0400
@@ -11,15 +11,6 @@
     #if $discard_threshold
         -t '$discard_threshold'
     #end if
-    #if $quick_filter
-        '$quick_filter'
-    #end if
-    #if $external_counter
-        '$external_counter'
-    #end if
-    #if $skip_length
-        -j '$skip_length'
-    #end if
     $input_fastqs.forward $input_fastqs.reverse
   ]]></command>
   <inputs>
@@ -33,12 +24,6 @@
     <param name="discard_threshold" type="float"
 	   label="Discard Threshold" help="A read of length L is discarded if it has at less than (L - k) * t hits to the same locus in the kmer database, where k is the kmer length. 0 &lt;= t &lt;= 1"
 	   value="0.3" min="0" max="1" />
-    <param name="quick_filter" type="boolean"
-	   label="Quick Filter" help="Quick filter; if the first, middle and last kmers of a read are not in the kmer DB, the read is discarded. Disabled by default."
-	   truevalue="-q" falsevalue="" optional="true" />
-    <param name="external_counter" type="boolean"
-	   label="External Kmer Counter" help="Use external kmc kmer counter. Disabled by default."
-	   truevalue="-e" falsevalue="" optional="true" />
     <param name="skip_length" type="integer"
 	   label="Skip Length" help="Skip length between consecutive k-mers."
 	   value="1" min="1" max="32" />
@@ -49,25 +34,6 @@
     <data name="output_file" format="tsv"/>
   </outputs>
   <help><![CDATA[
-    usage: MentaLiST.jl call -o O -s S --db DB [-t T] [-q] [-e] [-j J] [-h] files...
-
-    positional arguments:
-    files       FastQ input files
-
-    optional arguments:
-    -o O        Output file with MLST call
-    -s S        Sample name
-    --db DB     Kmer database
-    -t T        A read of length L is discarded if it has at less than
-                (L - k) * t hits to the same locus in the kmer database,
-                where k is the kmer length. 0 <= t <= 1 (type: Float64,
-                default: 0.3
-    -q          Quick filter; if the first, middle and last kmers of a
-                read are not in the kmer DB, the read is discarded.
-                Disabled by default.
-    -e          Use external kmc kmer counter. Disabled by default.
-    -j J        Skip length between consecutive k-mers. Defaults to 1.
-    -h, --help  show this help message and exit
   ]]></help>
   <citations>
     <citation type="doi">10.1101/172858</citation>