diff krocus.xml @ 0:d3ccbecf8f7f draft

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 15e535fd467e72874790ae7efd039237709b11ba-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/krocus.xml	Thu Feb 07 12:02:43 2019 -0500
@@ -0,0 +1,79 @@
+<tool id="krocus" name="krocus" version="@VERSION@">
+    <description>Multi-locus sequence typing (MLST) from uncorrected long reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        krocus 
+        --output_file detected_mlst.tsv
+        #if str($opt_args.filtered_reads_file) != ""
+            --filtered_reads_file $opt_args.filtered_reads_file
+        #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
+        
+        #if $opt_args.divisible_by_3
+            --divisible_by_3
+        #end if
+        
+        #if $opt_args.verbose
+            --verbose
+        #end if
+
+        '$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 argument="--filtered_reads_file" type="text" value="" optional="True" label="Filename to save matching reads to" help="Default: None" />
+        <param argument="--max_gap" type="integer" 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" value="10" label="Flanking region around a block to use for mapping" help="Default:10" />
+        <param argument="--min_block_size" type="integer" value="150" label="Minimum block size in bases" help="Default:150" />
+        <param argument="--min_fasta_hits" type="integer" value="10" label="Minimum No. of kmers matching a read" help="Default:10" />
+        <param argument="--min_kmers_for_onex_pass" type="integer" value="5" label="Minimum No. of kmers matching a read in 1st pass" help="Default:5" />
+        <param argument="--max_kmers" type="integer" value="10" label="Dont count kmers occuring more than this many times" help="Default:10" />
+        <param argument="--print_interval" type="integer" value="10" label="Print ST every this number of reads" help="(Default:500)" />
+        <param argument="--kmer" type="integer" 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="--target_st" type="integer" value="" optional="True" label="For performance testing print time to find given ST" help="(Default:None)" />
+        <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"/>
+    </outputs>
+
+    <tests>
+        <test>
+        <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="contains" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+    usage: krocus [options] allele_directory input.fastq
+
+    multi-locus sequence typing (MLST) from uncorrected long reads
+    
+    Documentation can be found at `<https://github.com/andrewjpage/krocus>`_.
+    ]]></help>
+ <expand macro="citations" />
+</tool>