view preprocessing.xml @ 24:431aebd93843 draft default tip

Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.

<tool id="rna_probing_preprocessing" version="1.0.0" name="Preprocessing" force_history_refresh="True">
    <description>RNA probing data</description>

    <requirements>
       <requirement type="package" version="4.1.0">gnu_awk</requirement>
       <requirement type="set_environment">RNA_RPOBING_SCRIPT_PATH</requirement>
    </requirements>

    <command interpreter="bash">
        preprocessing.sh

        ## check if paired-end
        #if str( $library.type ) == "paired"
            -2 $library.input2
        #end if

        ## Inputs
        -1 $library.input1

        ## Barcode sequence
        -b '$library.barcode_seq'

        ## Trimming length
        -t $trim
    </command>

    <inputs>
	<!-- single/paired -->
        <conditional name="library">
            <param name="type" type="select" label="Is this single or paired-end sequencing?">
                <option value="single">Single-end</option>
                <option value="paired">Paired-end</option>
            </param>
            <when value="single">
                <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="Must have Sanger-scaled quality values (fastqsanger)." />
                <param name="barcode_seq" type="text" size="20" label="Barcode sequence" help="Reads that do not start with the signature will be removed. Use IUPAC alphabet, e.g. NNNNXRTYNN as in the randomized part of the ligation adapter." >
    <!--		    <validator type="empty_field" message="Specify the Barcode sequence" /> -->
                </param>
            </when>
            <when value="paired">
                <param format="fastqsanger" name="input1" type="data" label="FASTQ file (read 1)" help="Must have Sanger-scaled quality values (fastqsanger)." />
                <param format="fastqsanger" name="input2" type="data" label="FASTQ file (read 2)" help="Must have Sanger-scaled quality values (fastqsanger)." />
                <param name="barcode_seq" type="text" size="20" label="Barcode sequence" help="Reads that do not start with the signature will be removed. Use IUPAC alphabet, e.g. NNNNXRTYNN as in the randomized part of the ligation adapter." >
                    <!-- <validator type="empty_field" message="Specify the Barcode sequence" /> -->
                </param>
            </when>
        </conditional>
        <param name="trim" type="integer" min="0" optional="true" value="15" label="3' trimming length" help="Number of random bases for random priming, will be removed as they are likely to differ from a template." />

    </inputs>

    <outputs>
        <data format="fastqsanger" name="output1" label="${tool.name} on ${on_string}: Read 1" from_work_dir="output_dir/read1.fastq" />
        <data format="fastqsanger" name="output2" label="${tool.name} on ${on_string}: Read 2" from_work_dir="output_dir/read2.fastq" >
            <filter> library['type'] == "paired"</filter>
        </data>
        <data format="tabular" name="barcodes" label="${tool.name} on ${on_string}: Barcodes" from_work_dir="output_dir/barcodes.txt">
            <!-- <filter> library['barcode_seq'] != '' </filter> -->
        </data>
    </outputs>

    <tests>
        <test>
            <param name="input1" value="reads1.fastq"/>
            <param name="input2" value="reads2.fastq"/>
            <param name="barcode_seq" value="NNNNNNN"/>
            <param name="trim" value="15"/>
            <output name="output1" file="reads1_preprocessed.fastq"/>
            <output name="output2" file="reads2_preprocessed.fastq"/>
            <output name="barcodes" file="barcodes.txt"/>
        </test>
    </tests>

    <help>
**What it does**

*Preprocessing* tool removes and saves the random barcodes sequences, if they were ligated to 3’ ends of cDNA, in a separate dataset to be used in downstream analysis. Additionally to debarcoding, it trims 1) the 5’ end of the second-in-pair reads to remove the reverse transcription primer derived sequence and 2) 3’ end of both reads to remove possible random barcode incorporation in the second-in-pair read and random primer in first-in-pair read.

------

**Examples**

Sample input files (quality scores omited)::

  * Read1
    @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296 1:N:0:ATCACG
    TTCGCACAACATNATGGAGGCTTCACGGTACAGAACGAGGCCAGCAAATACCAAGTCTCAGTGAACAAATACAAAGGGACGGCTGGCAACGCCCTCAT
    @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461 1:N:0:ATCACG
    ACCCCGCATCAAATTGGGAACTACTTCCAGCAGTTGTTAGACTTGGGCTCTGGCAGCCCCTTGGAGTGGAGGGACTTGCAGCCCTTCTTATCAGGTCT

  * Read2
    @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296 2:N:0:ATCACG
    CACAAATCTGCCGTTTGGATTGGCTGCATGGCATCTGTTATACCACCAGCCACCACCATCTTCTTTGGAGCACTGTTTTCTTGGATCCGTAGTTACCC
    @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461 2:N:0:ATCACG
    GTTGGGGGTGTGGGGAAAAAAATAAAAATCGTGAGAAGTTTTAAGACTATGTCACAAAAATGGCTTTAATTATACCATCAAACAGAAACCACCAATTG

Run 1 - Barcode Sequence = '', Trimming length = 10::

  * Read1
    @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296
    TTCGCACAACATNATGGAGGCTTCACGGTACAGAACGAGGCCAGCAAATACCAAGTCTCAGTGAACAAATACAAAGGGACGGCTGGCA
    @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461
    ACCCCGCATCAAATTGGGAACTACTTCCAGCAGTTGTTAGACTTGGGCTCTGGCAGCCCCTTGGAGTGGAGGGACTTGCAGCCCTTCT

  * Read2
    @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296
    CCGTTTGGATTGGCTGCATGGCATCTGTTATACCACCAGCCACCACCATCTTCTTTGGAGCACTGTTTTCTTGGATCCGTAGTTACCC
    @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461
    TGGGGAAAAAAATAAAAATCGTGAGAAGTTTTAAGACTATGTCACAAAAATGGCTTTAATTATACCATCAAACAGAAACCACCAATTG

Run 2 - Barcode Sequence = 'NNNNNNN', Trimming length = 10::

  * Read1
    @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296
    AACATNATGGAGGCTTCACGGTACAGAACGAGGCCAGCAAATACCAAGTCTCAGTGAACAAATACAAAGGGACGGCTGGCA
    @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461
    ATCAAATTGGGAACTACTTCCAGCAGTTGTTAGACTTGGGCTCTGGCAGCCCCTTGGAGTGGAGGGACTTGCAGCCCTTCT

  * Read2
    @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296
    CCGTTTGGATTGGCTGCATGGCATCTGTTATACCACCAGCCACCACCATCTTCTTTGGAGCACTGTTTTCTTGGATCCGTA
    @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461
    TGGGGAAAAAAATAAAAATCGTGAGAAGTTTTAAGACTATGTCACAAAAATGGCTTTAATTATACCATCAAACAGAAACCA

  * Barcodes

    @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296        TTCGCAC
    @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461        ACCCCGC

    </help>

    <citations>
        <citation type="doi">10.1093/nar/gku167</citation>
    </citations>

</tool>