annotate sinto_barcode.xml @ 3:fb61eb03e313 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit 4a156b17a386e1ecf13dfb2b232a1fc7d8344adc

<tool id="sinto_barcode" name="Sinto barcode" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>add cell barcodes to FASTQ read names</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">sinto</requirement>
    </requirements>
    <version_command>sinto --version</version_command>
    <command><![CDATA[
    ln -s '$barcode_fastq' barcodes.fastq.gz &&
    ln -s '${fastq_input.read1_fastq}' read1.fastq.gz &&
    #if str( $fastq_input.fastq_input_selector ) == "paired":
    ln -s '${fastq_input.read2_fastq}' read2.fastq.gz &&
    #end if
    sinto barcode
    --barcode_fastq barcodes.fastq.gz
    --read1 read1.fastq.gz
    #if str( $fastq_input.fastq_input_selector ) == "paired":
    --read2 read2.fastq.gz
    #end if
    --bases $bases
]]>    </command>
    <inputs>
        <param type="data" name="barcode_fastq" format="fastqsanger.gz" label="FASTQ file containing cell barcode sequences" />
        <conditional name="fastq_input">
            <param name="fastq_input_selector" type="select" label="Single or Paired-end data">
                <option value="paired">Paired</option>
                <option value="single">Single</option>
            </param>
            <when value="paired">
                <param name="read1_fastq" type="data" format="fastqsanger.gz" label="Forward reads FASTQ file" />
                <param name="read2_fastq" type="data" format="fastqsanger.gz" label="Reverse reads FASTQ file" />
            </when>
            <when value="single">
                <param name="read1_fastq" type="data" format="fastqsanger.gz" label="Select FASTQ file" />
            </when>
        </conditional>
        <param type="integer" name="bases" value="16" min="0" label="Number of bases to extract from barcode-containing FASTQ" />
    </inputs>
    <outputs>
        <data name='read1_out' format='fastqsanger.gz' label="${tool.name} on ${on_string}: barcoded read 1" from_work_dir="read1.barcoded.fastq.gz" />
        <data name='read2_out' format='fastqsanger.gz' label="${tool.name} on ${on_string}: barcoded read 2" from_work_dir="read2.barcoded.fastq.gz" >
            <filter>fastq_input['fastq_input_selector'] == 'paired'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="barcode_fastq" value="barcodes.fastq.gz" />
            <param name="fastq_input_selector" value="single"/>
            <param name="read1_fastq" value="read1.fastq.gz" />
            <output name="read1_out" file="read1.barcoded.fastq.gz" ftype="fastqsanger.gz"  decompress="true" />
        </test>
        <test expect_num_outputs="2">
            <param name="barcode_fastq" value="barcodes.fastq.gz" />
            <param name="fastq_input_selector" value="paired"/>
            <param name="read1_fastq" value="read1.fastq.gz" />
            <param name="read2_fastq" value="read2.fastq.gz" />
            <output name="read1_out" file="read1.barcoded.fastq.gz" ftype="fastqsanger.gz"  decompress="true"/>
            <output name="read2_out" file="read2.barcoded.fastq.gz" ftype="fastqsanger.gz"  decompress="true"/>
        </test>
    </tests>
    <help><![CDATA[

Sinto is a toolkit for processing aligned single-cell data.
--------------------------------------------------------------------------------------------------------------
Cell barcodes from one FASTQ file added to the read names of another, or the same, FASTQ file. This is useful when processing raw single-cell sequencing data, as the cell barcode information can easily be propagated to the aligned BAM file by encoding the cell barcode in the read name.

**Inputs**
FASTQ files containing barcodes and forward reads. An optional reverse reads FASTQ file can be provided for paired-end experiments. Note that all the FASTQs must contain the same number of reads and the reads must appear in the same order.

**Outputs**
FASTQ files with the read names modified to contain the cell barcode sequence at the beginning of the read name, separated from the original read name by a : character.

    ]]>    </help>
    <expand macro="citations" />
</tool>