view fairy_sketch.xml @ 0:666cf1a9572c draft default tip

planemo upload for repository https://github.com/bluenote-1577/fairy commit bfba48480e14ad877a96476ef1a9d6973e1129f6

<tool id="fairy_sketch" name="Fairy sketch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>sketching of k-mers for coverage into a hashtable</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
        
            #import re

            mkdir -p res &&

            #if $input.is_select == "single":
                #set $file = re.sub('[^\s\w\-\\.]', '_', str($reads.element_identifier))
                #set $filename = $file + '.bcsp'
                ln -s '$reads' '$file' &&
            #else if $input.is_select == 'pair':
                #set $file_1 = re.sub('[^\s\w\-\\.]', '_', str($first_pairs.element_identifier))
                #set $file_2 = re.sub('[^\s\w\-\\.]', '_', str($second_pairs.element_identifier))
                ## Since the tool used the first inputed file to name the output file this has to be used there to cp the right file 
                #set $filename = $file_1 + '.paired.bcsp'
                ln -s '$first_pairs' '$file_1' &&
                ln -s '$second_pairs' '$file_2' &&
            #else
                #set $file_1 = re.sub('[^\s\w\-\\.]', '_', str($paired_collection.forward.element_identifier))
                #set $file_2 = re.sub('[^\s\w\-\\.]', '_', str($paired_collection.reverse.element_identifier))
                ## Since the tool used the first inputed file to name the output file this has to be used there to cp the right file 
                #set $filename = $file_1 + '.paired.bcsp'
                ln -s '$paired_collection.forward' '$file_1' &&
                ln -s '$paired_collection.reverse' '$file_2' &&
            #end if

            fairy sketch
            -t "\${GALAXY_SLOTS:-3}"
            -c ${c}
            -k ${k}
            -d 'res'
            #if $input.is_select == "single":
                -r '$file'
            #else
                -1 '$file_1'
                -2 '$file_2'
            #end if
            &&

            cp './res/${filename}' '$output'

        ]]>
    </command>
    <inputs>
        <conditional name="input">
            <param name="is_select" type="select" label="Single or paired-end reads">
                <option value="single">Single</option>
                <option value="pair">Paired</option>
                <option value="paired_collection">Paired collection</option>
            </param>
            <when value="single">
                <param argument="--reads" type="data" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" label="Input single-end reads"/>
            </when>
            <when value="pair">
                <param argument="--first_pairs" type="data" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" label="Input first paired-end reads"/>
                <param argument="--second_pairs" type="data" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" label="Input second paired-end reads"/>
            </when>
            <when value="paired_collection">
                <param name="paired_collection" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" type="data_collection" collection_type="paired" label="Input paired collection reads"/>
            </when>
        </conditional>
        <param argument="-c" type="integer" value="50" optional="true" label="Set the subsampling rate"/>
        <param argument="-k" type="select" label="Select k-mer size">
            <option value="31">31</option>
            <option value="21">21</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="bcsp" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <conditional name="input">
                <param name="is_select" value="single"/>
                <param name="reads" value="single_test.fasta.gz" ftype="fasta.gz"/>
            </conditional>
            <output name="output" file="single_test.fasta.gz.bcsp"/>
        </test>
        <test>
            <conditional name="input">
                <param name="is_select" value="pair"/>
                <param name="first_pairs" value="test_paired_1.fq.gz" ftype="fastq.gz"/>
                <param name="second_pairs" value="test_paired_2.fq.gz" ftype="fastq.gz"/>
            </conditional>
            <output name="output" file="test_paired_1.fq.gz.paired.bcsp"/>
        </test>
        <test>
            <conditional name="input">
                <param name="is_select" value="paired_collection"/>
                <param name="paired_collection">
                    <collection type="paired">
                        <element name="forward" value="test_paired_1.fq.gz" ftype="fastq.gz" />
                        <element name="reverse" value="test_paired_2.fq.gz" ftype="fastq.gz" />
                    </collection>
                </param>    
            </conditional>
            <output name="output" file="forward.paired.bcsp"/>
        </test>
    </tests>
    <help>
        <![CDATA[

        This tool sketch the k-mer into a hashtable which will be needed for the fairy coverage tool to create the coverage file.

        .. class:: infomark

            This tool can either use single-end or paired-end reads as input in multiple file formats.
        ]]>
    </help>
    <expand macro="citations"/>
</tool>