<tool id="mitobim" name="MITObim" version="0.1.0">
    <description>mitochondrial baiting and iterative mapping</description>
    <requirements>
        <requirement type="package" version="4.0.2">mira4_assembler</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
	cp $readpool readpool.fastq;
        MITObim_1.8.pl
        	--pair
        	--quick $quick
        	-start 1
        	-end $end
        	-sample $sample
        	-ref $ref
        	-readpool readpool.fastq
        	--clean >& log;
	rm readpool.fastq
    ]]></command>
    <inputs>
        <param type="data" name="quick" format="fasta,txt" 
        	   label="starts process with initial baiting using provided fasta reference" />
        <param type="data" name="readpool" format="fastqsanger,fastq" 
        	   label="readpool in fastq format (*.gz is also allowed) ! For pair-end reads, please use interleave tool to join the forward and revers reads into one fastq file. !" />
        <param name="end" type="integer" label="iteration to end with, default=1" 
               value="50" min="1" max="500" help="(-end)" />
        <param name="sample" size="30" type="text" value="sample" label="sampleID as used in initial MIRA assembly"/>       
        <param name="ref" size="30" type="text" value="reference" label="referenceID as used in initial MIRA assembly"/>       
    </inputs>
    <outputs>
        <data name="output1" format="fasta" from_work_dir="finaloutput.fasta" label="${tool.name} on ${on_string}: Fasta"/>
	<data name="output2" format="txt" from_work_dir="log" label="${tool.name} on ${on_string}: Log" />
    </outputs>

    <help><![CDATA[
        
MITObim - mitochondrial baiting and iterative mapping
version 1.8
author: Christoph Hahn, (c) 2012-2015

usage: ./MITObim.pl <parameters>

parameters:
        -start <int>        iteration to start with, default=1
        -end <int>      iteration to end with, default=1
        -sample <string>    sampleID as used in initial MIRA assembly
        -ref <string>       referenceID as used in initial MIRA assembly
        -readpool <FILE>    readpool in fastq format (*.gz is also allowed)
        -maf <FILE>     maf file from previous MIRA assembly

optional:
        --quick <FILE>      starts process with initial baiting using provided fasta reference
        --kbait <int>       set kmer for baiting stringency (default: 31)
        --denovo        runs MIRA in denovo mode (default: mapping)
        --pair          finds pairs after baiting (relies on /1 and /2 header convention for read pairs) (default: no)
        --verbose       show detailed output of MIRA modules (default: no)
        --split         split reference at positions with more than 5N (default: no)
        --help          shows this helpful information
        --clean                 retain only the last 2 iteration directories (default: no)
        --trimreads     trim data (default: no; we recommend to trim beforehand and feed MITObim with pre trimmed data)
        --trimoverhang      trim overhang up- and downstream of reference (default: no)
        --missmatch <int>   number of allowed missmatches in mapping - only for illumina data (default: 15% of avg. read length)
        --min_cov <int>     minimum average coverage of contigs to be retained (default: off)
        --mirapath <string>     full path to MIRA binaries (only needed if MIRA is not in PATH)
        --iontor        use iontorrent data (experimental - default is illumina data)
        --454           use 454 data (experimental - default is illumina data)

examples:
        ./MITObim.pl -start 1 -end 5 -sample StrainX -ref reference-mt -readpool illumina_readpool.fastq -maf initial_assembly.maf
        ./MITObim.pl -end 10 --quick reference.fasta -sample StrainY -ref reference-mt -readpool illumina_readpool.fastq


    ]]></help>

</tool>