<tool id="rcorrector" name="RNA-seq Rcorrector" version="1.0.3+galaxy1">
    <description>a kmer-based error correction method for RNA-seq data</description>
    <requirements>
        <requirement type="package" version="1.0.3">rcorrector</requirement>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $library.lib == "single":
            ln -s '$library.input1' input_1.fq &&
        #end if
        #if $library.lib == "paired":
            ln -s '$library.input1' input_1.fq && ln -s '$library.input2' input_2.fq &&
        #end if
        run_rcorrector.pl
        #if $library.lib == "single":
            -s input_1.fq
        #end if
        #if $library.lib == "paired":
            -1 input_1.fq -2 input_2.fq
        #end if
        -k '$advanced.kmers' -t \${GALAXY_SLOTS:-4} -maxcorK '$advanced.maxcorK' -wk '$advanced.wk' -ek '$advanced.ek' -od output_file_directory

        #if $library.lib == "paired":
            #if $library.filter:
                && python '$__tool_directory__/FilterUncorrectabledPEfastq.py'
                -1 output_file_directory/input_1.cor.fq -2 output_file_directory/input_2.cor.fq -o fixed 2>&1 > rmunfixable.log && cat rmunfixable.log
            #end if
        #end if
    ]]></command>
    <inputs>
        <conditional name="library">
            <param name="lib" type="select" label="Is this library paired- or single-end?">
                <option value="single">single</option>
                <option value="paired" selected="True">paired</option>
            </param>
            <when value="single">
                <param type="data" name="input1" label="FastQ file" format="fastq,fastqsanger" />
            </when>
            <when value="paired">
                <param type="data" name="input1" label="FastQ file R1 (left)" format="fastq,fastqsanger" />
                <param type="data" name="input2" label="FastQ file R2 (right)" format="fastq,fastqsanger" />
                <param name="filter" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Filter uncorrectable reads" help="This will run FilterUncorrectabledPEfastq and remove uncorrectable reads."/>
            </when>
        </conditional>
        <conditional name="advanced">
            <param name="adv" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Additional options"/>
            <when value="TRUE">
                <param name="kmers" label="kmer length" value="23" max="32" type="integer" help="(smaller 33, default: 23)"/>
                <param name="maxcorK" label="max correction within k-bp window" value="4" type="integer" help="the maximum number of correction within k-bp window (default: 4)"/>
                <param name="wk" label="estimate weak kmer count" value="0.95" type="float" help="the proportion of kmers that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95)"/>
                <param name="ek" label="expected number of kmers" value="100000000" type="integer" help="expected_number_of_kmers: does not affect the correctness of program but affect the memory usage (default: 100000000)"/>
            </when>
            <when value="FALSE">
                <param name="kmers" value="23" type="hidden"/>
                <param name="maxcorK" value="4" type="hidden"/>
                <param name="wk" value="0.95" type="hidden"/>
                <param name="ek" value="100000000" type="hidden"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output1" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="output_file_directory/input_1.cor.fq">
            <filter>library['lib'] == 'single'</filter>
        </data>
        <data name="output2" format="fastq" label="${tool.name} on ${on_string}: cor R1" from_work_dir="output_file_directory/input_1.cor.fq">
            <filter>library['lib'] == 'paired' and library['filter'] is False</filter>
        </data>
        <data name="output3" format="fastq" label="${tool.name} on ${on_string}: cor R2" from_work_dir="output_file_directory/input_2.cor.fq">
            <filter>library['lib'] == 'paired' and library['filter'] is False</filter>
        </data>
        <data name="output4" format="fastq" label="${tool.name} on ${on_string}: fixed R1" from_work_dir="fixed_input_1.cor.fq">
            <filter>library['lib'] == 'paired' and library['filter']</filter>
        </data>
        <data name="output5" format="fastq" label="${tool.name} on ${on_string}: fixed R2" from_work_dir="fixed_input_2.cor.fq">
            <filter>library['lib'] == 'paired' and library['filter']</filter>
        </data>
    </outputs>
	<tests>
        <test>
            <conditional name="library">
                <param name="lib" value="paired"/>
                <param name="input1" value="sample_read1.fq" ftype="fastq"/>
                <param name="input2" value="sample_read2.fq" ftype="fastq"/>
            </conditional>
            <conditional name="advanced">
                <param name="kmers" value="23"/>
                <param name="maxcorK" value="4"/>
                <param name="wk" value="0.95"/>
                <param name="ek" value="100000000"/>
            </conditional>
            <output name="output2" file="sample_read1.cor.fq" ftype="fastq"/>
            <output name="output3" file="sample_read2.cor.fq" ftype="fastq"/>
        </test>
        <test>
            <conditional name="library">
                <param name="lib" value="paired"/>
                <param name="input1" value="sample_read1.fq" ftype="fastq"/>
                <param name="input2" value="sample_read2.fq" ftype="fastq"/>
                <param name="filter" value="TRUE"/>
            </conditional>
            <conditional name="advanced">
                <param name="kmers" value="23"/>
                <param name="maxcorK" value="4"/>
                <param name="wk" value="0.95"/>
                <param name="ek" value="100000000"/>
            </conditional>
            <output name="output2" file="fixed_sample_read1.cor.fq" compare="sim_size"/>
            <output name="output3" file="fixed_sample_read2.cor.fq" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

What is Rcorrector?

Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.
Rcorrector can also be applied to other type of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.

Uncorrectable paired-end reads can be removed using FilterUncorrectabledPEfastq.

More informations, see citations.

    ]]>
    </help>
    <citations>
        <citation type="doi">10.1186/s13742-015-0089-y</citation>
        <citation type="bibtex">
            @misc{githubFilterUncorrectabledPEfastq,
            author = {Adam H. Freedman},
            year = {2016},
            title = {FilterUncorrectabledPEfastq},
            publisher = {GitHub},
            journal = {GitHub repository},
            url = {https://github.com/harvardinformatics/TranscriptomeAssemblyTools/blob/master/FilterUncorrectabledPEfastq.py}
            }
        </citation>
    </citations>
</tool>