view read-it-and-keep.xml @ 0:554aa2a63f04 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"

<tool id="read_it_and_keep" name="Read It and Keep" version="@TOOL_VERSION@+galaxy0" profile="20.09">
    <macros>
        <token name="@FASTQ_FORMATS@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
        <token name="@TOOL_VERSION@">0.1.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">read-it-and-keep</requirement>
        <requirement type="package">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $ref_source.source == "history"
            ln -s '$ref_source.ref_fasta' ref${trim_reference}.fasta &&
        #elif $ref_source.source == "builtin"
            ln -s '$ref_source.ref_fasta_builtin.path' ref${trim_reference}.fasta &&
        #end if
        #if $trim_reference
            python '$__tool_directory__/trim_reference.py' ref${trim_reference}.fasta ref.fasta &&
        #end if
        #if $reads.read_type == "paired"
            ln -s '$reads.read1' read1.fastq &&
            ln -s '$reads.read2' read2.fastq &&
        #elif $reads.read_type == 'paired_collection'
            ln -s '$reads.paired_reads.forward' read1.fastq &&
            ln -s '$reads.paired_reads.reverse' read2.fastq &&
        #elif $reads.read_type == 'single'
            ln -s '$reads.single_read1' read1.fastq &&
        #end if
        readItAndKeep
            --tech $sequencing_tech
            --ref_fasta ref.fasta
            --min_map_length $adv.min_map_length
            --min_map_length_pc $adv.min_map_length_pc
            --reads1 read1.fastq
            #if $reads.read_type != "single"
                --reads2 read2.fastq
            #end if
            -o output
            #if $reads.read_type == 'single'
                && mv output.reads.fastq.gz output.reads_1.fastq.gz
            #end if
    ]]></command>
    <inputs>
        <conditional name="reads">
            <param type="select" label="Read type" name="read_type">
                <option value="paired" selected="true">Paired end</option>
                <option value="paired_collection">Paired collection</option>
                <option value="single">Single ended</option>
            </param>
            <when value="paired">
                <param type="data" format="@FASTQ_FORMATS@" name="read1" label="Read1" />
                <param type="data" format="@FASTQ_FORMATS@" name="read2" label="Read2" />
            </when>
            <when value="paired_collection">
                <param type="data_collection" collection_type="paired" format="@FASTQ_FORMATS@" name="paired_reads" label="Reads" />
            </when>
            <when value="single">
                <param type="data" format="@FASTQ_FORMATS@" name="single_read1" label="Read1" />
            </when>
        </conditional>
        <conditional name="ref_source">
            <param type="select" label="Reference genome source" name="source">
                <option value="history" selected="true">History</option>
                <option value="builtin">Built-in</option>
            </param>
            <when value="history">
                <param type="data" format="fasta" name="ref_fasta" label="Reference genome" />
            </when>
            <when value="builtin">
                <param type="select" name="ref_fasta_builtin" label="Reference genome">
                    <options from_data_table="all_fasta" />
                </param>
            </when>
        </conditional>
        <param type="boolean" name="trim_reference" label="Trim trailing As from the reference sequence" checked="true" truevalue="_untrimmed" falsevalue="" help="Remove all As at the end of the reference sequence to ensure that the reference has no poly-A tail (see Note in the general help section below)" />
        <param type="select" argument="--tech" name="sequencing_tech" label="Sequencing technology">
            <option value="illumina">Illumina</option>
            <option value="ont">Oxford Nanopore</option>
        </param>
        <section name="adv" title="Advanced options">
            <param argument="--min_map_length" type="integer" min="0" value="50" label="Shortest match required to keep a read (in bp)" />
            <param argument="--min_map_length_pc" type="float" min="0.0" max="100.0" value="50.0" label="Minimum length of match required to keep a read (as percentage of read length" />
        </section>
    </inputs>
    <outputs>
        <data name="output_reads1" format="fastqsanger.gz" label="Filtered reads ${on_string} - reads1" from_work_dir="output.reads_1.fastq.gz">
            <filter>reads["read_type"] == "single" or reads["read_type"] == "paired"</filter>
        </data>
        <data name="output_reads2" format="fastqsanger.gz" label="Filtered reads ${on_string} - reads2" from_work_dir="output.reads_2.fastq.gz">
            <filter>reads["read_type"] == "paired"</filter>
        </data>
        <collection type="paired" format="fastqsanger.gz" name="output_collection" label="Filtered reads ${on_string}">
            <filter>reads["read_type"] == "paired_collection"</filter>
            <data name="forward" format="fastqsanger.gz" from_work_dir="output.reads_1.fastq.gz" />
            <data name="reverse" format="fastqsanger.gz" from_work_dir="output.reads_2.fastq.gz" />
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <conditional name="reads">
                <param name="read_type" value="paired" />
                <param name="read1" value="test1.fastq.gz" ftype="fastqsanger.gz" />
                <param name="read2" value="test2.fastq.gz" ftype="fastqsanger.gz" />
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="illumina" />
            <output name="output_reads1" value="output_test1.fastq.gz" />
            <output name="output_reads2" value="output_test2.fastq.gz" />
        </test>
        <test expect_num_outputs="3">
            <conditional name="reads">
                <param name="read_type" value="paired_collection" />
                <param name="paired_reads">
                    <collection type="paired">
                        <element name="forward" value="test1.fastq.gz" ftype="fastqsanger.gz" />
                        <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger.gz" />    
                    </collection>
                </param>
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="illumina" />
            <output_collection name="output_collection">
                <element name="forward" value="output_test1.fastq.gz" />
                <element name="reverse" value="output_test2.fastq.gz" />
            </output_collection>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reads">
                <param name="read_type" value="single" />
                <param name="single_read1" value="test3.fastq.gz" ftype="fastqsanger.gz"/>
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="ont" />
            <output name="output_reads1" value="output_test3.fastq.gz" />
        </test>
    </tests>
    <help><![CDATA[
ReadItAndKeep
-------------

ReadItAndKeep is a tool for filtering viral sequence data to remove host reads, developed for cleaning
SARS-CoV-2 sequencing data. It maps reads against the SARS-CoV-2 viral genome (with the poly-A tail removed)
and only keeps those that map well.

**Note**: If the reference genome supplied contains a poly-A tail, reads that contain part of a poly-A tail will map
to the refence, no matter what species they originate from. If you are not sure if the reference you are using has had
trailing A's trimmed, enable the `Trim trailing As` option.

Input can be either Illumina or Oxford Nanopore reads.
    ]]></help>
    <citations>
        <citation type="doi">10.1101/2022.01.21.477194</citation>
    </citations>
</tool>