<tool id="migmap" name="MiGMAP" version="1.0.2.2">
    <description>mapper for full-length T- and B-cell repertoire sequencing
    </description>
    <requirements>
        <requirement type="package" version="1.0.2">migmap</requirement>
    </requirements>
    <command detect_errors='exit_code'><![CDATA[
export IGBLAST_PATH=\$(dirname \$(which igblastn)) &&
mkdir -p temp_db/igblast &&
ln -s "\${IGBLAST_PATH}/../share/igblast/bin/" ./temp_db/igblast &&
ln -s "\${IGBLAST_PATH}/../share/igblast/internal_data/" ./temp_db/igblast &&
ln -s "\${IGBLAST_PATH}/../share/igblast/optional_file/" ./temp_db/igblast &&

#if $input.is_of_type('fasta') :
    ln -s '$input' in.fa &&
#else
    ln -s '$input' in.fq &&
#end if
migmap 
    $allow_incomplete
    $allow_no_cdr3
    $allow_noncanonical
    $allow_noncoding
    $all_alleles
    $by_read
    #if str($qual_threshold):
        -q $qual_threshold
    #end if
    -p "\${GALAXY_SLOTS:-4}"
    --data-dir ./temp_db/igblast/
    -S $species 
    -R $receptor_list
    #if $input.is_of_type('fasta'): 
        in.fa
    #else
        in.fq
    #end if
    '$output'
    ]]></command>
    <inputs>
        <param type="data" name="input" format="fasta,fastq"/>
        <param type="select" name="species" label="Species" value='human'>
            <option value='human' selected='true'>Human</option>
            <option value='mouse'>Mouse</option>
            <option value='rat'>Rat</option>
            <option value='rabbit'>Rabbit</option>
            <option value='rhesus_monkey'>Rhesus monkey</option>
        </param>
        <param type="select" name="receptor_list" label="Receptor and Chain" multiple='true' value='IGH'>
            <option value='IGH' selected='true'>IGH</option>
            <option value='IGL'>IGL</option>
            <option value='IGK'>IGK</option>
            <option value='TRA'>TRA</option>
            <option value='TRB'>TRB</option>
            <option value='TRG'>TRG</option>
            <option value='TRD'>TRD</option>
        </param>
        <param name="qual_threshold" type="integer" label="Quality Theshold" optional="true"
           help="Threshold for average quality of mutations and N-regions of CDR3 (only relevant for fastq input)"/>
        <param name="allow_incomplete" type="boolean" label="Report clonotypes with partial CDR3 mapping" checked="false"
           truevalue="--allow-incomplete" falsevalue=""/>
        <param name="all_alleles" type="boolean"
           label="use all alleles during alignemt (default = only major (*01) alleles)" checked='false'
           truevalue="--all-alleles" falsevalue=""/>
        <param name="allow_no_cdr3" type="boolean" label="Report clonotypes with no CDR3" checked='false'
           truevalue="--allow-no-cdr3" falsevalue=""/>
        <param name="allow_noncanonical" type="boolean" label="Report clonotypes that have non-canonical CDR3"
           checked='false'
           truevalue="--allow-noncanonical" falsevalue=""/>
        <param name="allow_noncoding" type="boolean" label="Report non-coding clonotypes (stop codon or frameshift)"
           checked='false'
           truevalue="--allow-noncoding" falsevalue=""/>
        <param name="by_read" type="boolean" label="Report mapping details for each read" checked='false'
           truevalue="--by-read" falsevalue=""/>
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="test_stop_codon.fa"/>
            <param name="allow_noncoding" value="--allow-noncoding"/>
            <param name="by_read" value="--by-read"/>
            <param name="allow_noncanonical" value="--allow-noncanonical"/>
            <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
            <param name="allow_incomplete" value="--allow-incomplete"/>
            <param name="all_alleles" value="--all-alleles"/>
            <output name="output" file="test_stop_codon.out"/>
        </test>
        <test>
            <param name="allow_noncoding" value="--allow-noncoding"/>
            <param name="by_read" value="--by-read"/>
            <param name="input" value="test_out_of_frame.fa"/>
            <output name="output" file="test_out_of_frame.out"/>
        </test>
    </tests>
    <help><![CDATA[

    This software is a smart wrapper for the IgBlast V-(D)-J mapping tool designed to facilitate analysis immune
    receptor libraries profiled using high-throughput sequencing

    ]]></help>
    <citations>
        <citation type="bibtex">
          @misc{githubmigmap,
          author = {Shugay, Mikhail},
          year = {2015},
          title = {migmap},
          publisher = {GitHub},
          journal = {GitHub repository},
          url = {https://github.com/mikessh/migmap},
          }
        </citation>
    </citations>
</tool>