# HG changeset patch
# User dfornika
# Date 1504651935 14400
# Node ID 071665c7c3441fd31bbf8059c98188a9b30b2dd3

planemo upload

diff -r 000000000000 -r 071665c7c344 tools/mentalist_build.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mentalist_build.xml	Tue Sep 05 18:52:15 2017 -0400
@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+<tool id="mentalist_build" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.2">
+  <requirements>
+    <requirement type="package" version="0.1.2">mentalist</requirement>
+  </requirements>
+  <command detect_errors="exit_code">
+  <![CDATA[
+	   mkdir mentalist-database && cd mentalist-database &&
+	   MentaLiST.jl
+	   build_db
+	   --db '$kmer_database'
+	   -k '$kmer_size'
+	   #if $profile
+	   -p '$profile'
+	   #end if
+	   -f ${" ".join(map(str, $input_fastas))} &&
+	   cd .. &&
+	   python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}'
+  ]]>
+  </command>
+  <inputs>
+    <param name="kmer_size" type="integer"
+	   label="Kmer size" help="Kmer size"
+	   value="31" min="1" max="32" />
+    <param name="input_fastas" type="data_collection" collection_type="list" format="fasta" multiple="true"
+	   label="Input Fasta" help="Fasta input files" />
+    <param name="profile" type="data" format="tsv" optional="true"
+	   label="Profile" help="Profile for known genotypes" />
+  </inputs>
+  <outputs>
+    <data name="out_file" format="data_manager_json" />
+  </outputs>
+  <citations>
+    <citation type="doi">10.1101/172858</citation>
+  </citations>
+</tool>
diff -r 000000000000 -r 071665c7c344 tools/mentalist_call.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mentalist_call.xml	Tue Sep 05 18:52:15 2017 -0400
@@ -0,0 +1,72 @@
+<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.2">
+  <requirements>
+    <requirement type="package" version="0.1.2">mentalist</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+  'MentaLiST.jl'
+  call
+  -o '$output_file'
+  -s '$sample_name'
+  --db '$kmer_db'
+  #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>
+    <param name="sample_name" type="text"
+	   label="Sample Name" help="Sample Name" />
+    <param name="kmer_db" type="data" format="h5"
+	   label="Kmer DB" help="Kmer database" />
+    <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" />
+    <param name="input_fastqs" type="data_collection" collection_type="paired" format="fastq"
+	   label="Input FastQ" help="FastQ input files" />
+  </inputs>
+  <outputs>
+    <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>
+  </citations>
+</tool>