--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/krocus.xml	Tue Mar 12 10:45:51 2024 +0000
@@ -0,0 +1,90 @@
+<tool id="krocus" name="krocus" version="@VERSION@">
+    <description>Multi-locus sequence typing (MLST) from uncorrected long reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">krocus</xref>
+    </xrefs>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        krocus 
+        --output_file detected_mlst.tsv
+        #if $opt_args.filtered_reads
+            --filtered_reads_file filtered_reads.fq
+        #end if
+        --max_gap $opt_args.max_gap
+        --min_kmers_for_onex_pass $opt_args.min_kmers_for_onex_pass
+        --margin $opt_args.margin
+        --min_block_size $opt_args.min_block_size
+        --min_fasta_hits $opt_args.min_fasta_hits
+        --min_kmers_for_onex_pass $opt_args.min_kmers_for_onex_pass
+        --max_kmers $opt_args.max_kmers
+        --print_interval $opt_args.print_interval
+        --kmer $opt_args.kmer        
+        $opt_args.divisible_by_3
+        $opt_args.verbose
+        '$krocus_mlst_databases.fields.path' '$fastq'
+    ]]>
+    </command>
+    <inputs>
+        <param name="fastq" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single read"/>
+        <param label="Select a database" name="krocus_mlst_databases" type="select">
+            <options from_data_table="krocus_mlst_databases">
+                <validator message="No database is available" type="no_options" />
+            </options>
+        </param>
+        <section name="opt_args" title="Optional Arguments">
+            <param name="filtered_reads" type="boolean" truevalue="true" falsevalue="" checked="false" label="Save filtered reads ?"/>
+            <param argument="--max_gap" type="integer" min="1" value="4" label="Maximum gap for blocks to be contigous, measured in
+                        multiples of the k-mer size" help="Default:4" />
+            <param argument="--margin" type="integer" min="1" value="10" label="Flanking region around a block to use for mapping" help="Default:10" />
+            <param argument="--min_block_size" type="integer" min="1" value="150" label="Minimum block size in bases" help="Default:150" />
+            <param argument="--min_fasta_hits" type="integer" min="1" value="10" label="Minimum No. of kmers matching a read" help="Default:10" />
+            <param argument="--min_kmers_for_onex_pass" type="integer" min="2" value="5" label="Minimum No. of kmers matching a read in 1st pass" help="Default:5" />
+            <param argument="--max_kmers" type="integer" min="1" value="10" label="Dont count kmers occuring more than this many times" help="Default:10" />
+            <param argument="--print_interval" type="integer" min="1" value="10" label="Print ST every this number of reads" help="(Default:500)" />
+            <param argument="--kmer" type="integer" min="2" value="10" label="k-mer size" help="(Default:11)" />
+            <param argument="--divisible_by_3" type="boolean" truevalue="--divisible_by_3" falsevalue="" checked="false" label="Genes which are not divisible by 3 are excluded" help="(Default:No)" />
+            <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on debugging" help="(Default:No)" />
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Output" from_work_dir="detected_mlst.tsv"/>
+        <data name="filtered_reads" format="fastq" label="${tool.name} on ${on_string}: Filtered reads" from_work_dir="filtered_reads.fq">
+            <filter>opt_args['filtered_reads'] is True</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="fastq" value="pacbio.fastq.gz" ftype="fastqsanger" />
+            <param name="krocus_mlst_databases" value="mlst_db"/>
+            <output name="output_file" ftype="tabular" file="mlst_output_pacbio.tsv" compare="sim_size" />
+        </test>
+        <test expect_num_outputs="2">
+            <param name="fastq" value="pacbio.fastq.gz" ftype="fastqsanger" />
+            <param name="filtered_reads" value="True" />
+            <param name="krocus_mlst_databases" value="mlst_db"/>
+            <output name="filtered_reads" ftype="fastq" file="filtered_reads.fq" compare="sim_size" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+    Multi-locus sequence typing (MLST) from uncorrected long reads
+
+    Krocus can predict a sequence type directly from uncorrected long reads, and
+    which was designed to consume read data as it is produced, providing results
+    in minutes. It is the only tool which can do this from uncorrected long
+    reads. We tested Krocus on over 600 samples sequenced with using long read
+    sequencing technologies from PacBio and Oxford Nanopore. It provides
+    sequence types on average within 90 seconds, with a sensitivity of 94% and
+    specificity of 97%, directly from uncorrected raw sequence reads.
+    
+    Documentation can be found at `<https://github.com/andrewjpage/krocus>`_.
+    ]]>
+    </help>
+    <expand macro="citations"/>
+</tool>