<tool id ="pyFastqJoiner" name="pyFastqJoiner">
    <requirements>
        <requirement type="package">pyCRAC</requirement>
    </requirements>
	<command interpreter="python"> 
	/usr/local/bin/pyFastqJoiner.py
	-f $ftype.f1 $ftype.f2
	-o $out
	--file_type=$ftype.type
	#if $joinc.ch == "-c":
        -c $joinc.c
    #end if#
	</command>
	<version_command>/usr/local/bin/pyFastqJoiner.py --version</version_command>
	<inputs>
		<conditional name="ftype">
            <param name="type" type="select" label="File type">
                <option value="fastq" selected="true">FASTQ</option>
                <option value="fasta">FASTA</option>
            </param>
            <when value="fastq">
                <param format="fastq" name="f1" type="data" label="First FastQ File -f" help="FastQ format" />
                <param format="fastq" name="f2" type="data" label="Second FastQ File -f" help="FastQ format" />
            </when>
            <when value="fasta">
                <param format="fasta" name="f1" type="data" label="First FastA File -f" help="FastA format" />
                <param format="fasta" name="f2" type="data" label="Second FastA File -f" help="FastA format" />
            </when>
		</conditional>
		<conditional name="joinc">
            <param name="ch" type="select"  label="Insert a character at join">
                <option value="" selected="true">NO</option>
                <option value="-c">YES</option>
            </param>
            <when value="-c">
                <param type="text" name="c" label="Add this character -c" value=":" >
                    <validator type="empty_field" message="enter a character or turn this option off" />
                </param>
            </when>
            <when value="">
            </when>
		</conditional>
	    <param name="label" type="text" format="txt" size="30" value="pyFastqJoiner" label="Enter output file label -o" />
	</inputs>
	<outputs>
		<data format="input" name="out" label="${label.value}.${ftype.type}"/>
            <change_format>
                <when input="ftype.type" value="fasta" format="fasta" />
            </change_format>
	</outputs>
	<help>

.. class:: infomark

**pyFastqJoiner**

pyFastqJoiner is part of the pyCRAC_ package. Merges paired sequences from two fastq or fasta formatted files.

Example::

    Forward reaction:
    
    @FCC102EACXX:3:1101:1343:2181#ATCACGAT/1##CAATAG
    CAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAAT
    +
    `efhYb][bdQQ`eeaeaYbeY^ceU__IXa[^ZYae
    @FCC102EACXX:3:1101:1424:2248#ATCACGAT/1##CCAGGA
    CTAACCATAAACTATGCCTACTAGGGATCCAGAGGTG
    +
    ^_adddhJbaehbedd`dIb_^cXaRI^BBBBBBBBB
    @FCC102EACXX:3:1101:1623:2036#ATCACGAN/1##CTCAGC
    CAAAGTTAGGGGATCGAAGATGATCAGATACCGTCGT
    +
    bghfc^YbgbeadggfdffeaS^ac_X^cegaGZ_ef
    @FCC102EACXX:3:1101:1574:2214#ATCACGAT/1##CGTTTT
    CTAATGACCCACTCGGCACCTTACGAAATCAAAGTCT
    +
    cdfgYY`cefhhZef\eaggXaceeghfQaeghWNW\
    
    Reverse reaction:
    
    @FCC102EACXX:3:1101:1343:2181#ATCACGAT/2
    AGCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAGA
    +
    YJaSJ`Z`K`YbSb[[daeJRR[YeWd_I^I^ecgc]OV\bdeaegbXb
    @FCC102EACXX:3:1101:1424:2248#ATCACGAT/2
    AAGTCCTTTAAGTTACAGCCTTGCGACCATACTACACCCAGAACCCAAA
    +
    YJJ\`JQY\`KJ`gY[[QRYY[[`H[_ceI^e[PYO^IWOHW^eaefhh
    @FCC102EACXX:3:1101:1623:2036#ATCACGAN/2
    GGCCAATCCTTATTGTGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTC
    +
    PP\`ccQ`eY[bQQ[d`ghehaghfgdg[`gb^bd[ePbH^c_c\a_eg
    
    Here the ":" character is used to split the two sequences. This character tells pyFastqSplitter where to split the sequences.
    This character is ignored by pyFastqDuplicateRemover
    
    Result:
    
    @FCC102EACXX:3:1101:1343:2181#ATCACGAT/1##CAATAG@FCC102EACXX:3:1101:1343:2181#ATCACGAT/2
    CAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAAT:AGCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAGA
    +
    `efhYb][bdQQ`eeaeaYbeY^ceU__IXa[^ZYaeYJaSJ`Z`K`YbSb[[daeJRR[YeWd_I^I^ecgc]OV\bdeaegbXb
    @FCC102EACXX:3:1101:1424:2248#ATCACGAT/1##CCAGGA@FCC102EACXX:3:1101:1424:2248#ATCACGAT/2
    CTAACCATAAACTATGCCTACTAGGGATCCAGAGGTG:AAGTCCTTTAAGTTACAGCCTTGCGACCATACTACACCCAGAACCCAAA
    +
    ^_adddhJbaehbedd`dIb_^cXaRI^BBBBBBBBBYJJ\`JQY\`KJ`gY[[QRYY[[`H[_ceI^e[PYO^IWOHW^eaefhh
    @FCC102EACXX:3:1101:1623:2036#ATCACGAN/1##CTCAGC@FCC102EACXX:3:1101:1623:2036#ATCACGAN/2
    CAAAGTTAGGGGATCGAAGATGATCAGATACCGTCGT:GGCCAATCCTTATTGTGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTC
    +
    bghfc^YbgbeadggfdffeaS^ac_X^cegaGZ_efPP\`ccQ`eY[bQQ[d`ghehaghfgdg[`gb^bd[ePbH^c_c\a_eg
       
.. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
        
------

**Parameter list**

Options::

    -f fastq_file1 fastq_file2	
                        Provide the names of two raw data files separated by a single space.
                        Make sure the first file is the data file of the forward (/1) sequencing reaction.

    --file_type=FASTQ     
                        Can join fasta and fastq files. Fastq is default
    
    -o mergedfastq.fastq, --outfile=mergedfastq.fastq
                        provide the name of the output file. By default it
                        will be printed to the standard output
    
    -c :  
                        This option adds the '|' character between the DNA
                        sequences so that it is much easier to split the data
                        again later on


	</help>
</tool>