comparison fastx_barcode_splitter.xml @ 4:015dc921d814 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1

3:8abdedf55101

<tool id="cshl_fastx_barcode_splitter" version="1.0.0" name="Barcode Splitter">
    <description></description>
    <requirements>
        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
    </requirements>
    <command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' </command>

    <inputs>
        <param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
        <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />

        <param name="EOL" type="select" label="Barcodes found at">
            <option value="--bol">Start of sequence (5' end)</option>
            <option value="--eol">End of sequence (3' end)</option>
        </param>

        <param name="mismatches" type="integer" value="2" label="Number of allowed mismatches" />

        <param name="partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" />
    </inputs>
    <outputs>
        <data format="html" name="output" />
    </outputs>
    <tests>
        <test>
            <!-- Split a FASTQ file -->
            <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
            <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
            <param name="EOL" value="Start of sequence (5' end)" />
            <param name="mismatches" value="2" />
            <param name="partial" value="0" />
            <output name="output" file="fastx_barcode_splitter1.out" />
        </test>
    </tests>
    <help>
**What it does**

This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria.

--------

**Output Example**

.. image:: barcode_splitter_output_example.png


------

This tool is based on `FASTX-toolkit`__ by Assaf Gordon.

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
    </help>
<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon ([e-mail]) -->
</tool>

4:015dc921d814

<tool id="cshl_fastx_barcode_splitter" version="1.0.1" name="Barcode Splitter">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
mkdir split &&
@CATS@ '$__tool_directory__/fastx_barcode_splitter.pl' --bcfile '$BARCODE'
--prefix 'split/'
--suffix '.$input.extension'
--mismatches $mismatches
--partial $partial
#if $refBarcodeLocation.barcodeLocation == "idxfile":
    --idxfile '$refBarcodeLocation.idxfile'
    --idxidstrip $refBarcodeLocation.idxidstrip
#else:
    $refBarcodeLocation.EOL
#end if
> '$summary'
    ]]></command>
    <inputs>
        <param name="BARCODE" type="data" format="txt" label="Barcodes to use" />
        <param name="input" type="data" format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" label="Library to split" />

        <conditional name="refBarcodeLocation">
            <param name="barcodeLocation" type="select" label="Barcodes found at">
                <option value="bol">Start of sequence (5' end)</option>
                <option value="eol">End of sequence (3' end)</option>
                <option value="idxfile">Separate index file</option>
            </param>
            <when value="bol">
                <param name="EOL" type="hidden" value="--bol" />
            </when>
            <when value="eol">
                <param name="EOL" type="hidden" value="--eol" />
            </when>
            <when value="idxfile">
                <param argument="--idxidstrip" type="integer" value="1" label="Characters to strip from the end of the sequence id before matching" />
                <param argument="--idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
            </when>
        </conditional>
        <param argument="--mismatches" type="integer" value="0" label="Number of allowed mismatches" />
        <param argument="--partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" />
    </inputs>

    <outputs>
        <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" />
        <collection name="split_output" type="list" format_source="input" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" />
        </collection>
    </outputs>

    <tests>
        <test>
            <!-- Split a FASTQ file -->
            <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
            <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
            <param name="barcodeLocation" value="bol" />
            <param name="mismatches" value="2" />
            <param name="partial" value="0" />
            <output name="summary" file="fastx_barcode_splitter1.out" />
            <output_collection name="split_output" type="list">
                <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
                <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
                <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
                <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
                <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
            </output_collection>
        </test>

        <test>
            <!-- Split a FASTQ file, using separate index read -->
            <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
            <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
            <param name="idxfile" value="fastx_barcode_splitter_index.fastq" ftype="fastqsolexa" />
            <param name="barcodeLocation" value="idxfile" />
            <param name="mismatches" value="2" />
            <param name="partial" value="0" />
            <output name="summary" file="fastx_barcode_splitter1.out" />
            <output_collection name="split_output" type="list">
                <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
                <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
                <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
                <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
                <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
            </output_collection>
        </test>
    </tests>

    <help><![CDATA[
**What it does**

This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria.

--------

**Output Example**

.. image:: barcode_splitter_output_example.png

------

This tool is based on `FASTX-toolkit`__ by Assaf Gordon.

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
    ]]></help>
    <expand macro="citations" />
<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon ([e-mail]) -->
</tool>