comparison masurca_simple.xml @ 1:86aa445e75d6 draft default tip

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0:0a33488ca043

    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #set $long = 'false'
        #if $nanopore_input.np_input == "Yes":
            #if $pacbio_input.pb_input == "Yes":
                cat '$nanopore_input.nano' '$pacbio_input.pacbio' > long.fastq.gz &&
            #else:
                ln -s '$nanopore_input.nano' long.fastq.gz &&
            #end if
            #set $long = 'true'
        #elif $pacbio_input.pb_input == "Yes":
            ln -s '$pacbio_input.pacbio' long.fastq.gz &&
            #set $long = 'true'
        #end if
        masurca -t \${GALAXY_SLOTS:-8} -i
        #if str( $illumina_input.input_type ) == "single"
            '$illumina_input.fastq_input1'

            '$illumina_input.fastq_input1','$illumina_input.fastq_input2'
        #elif str( $illumina_input.input_type ) == "paired_collection"
            '$illumina_input.fastq_input1','$illumina_input.fastq_input2'
        #end if
        #if $long == "true":
            -r long.fastq.gz
        #end if
    ]]></command>
    <inputs>
        <conditional name="illumina_input">
            <param name="input_type" type="select" label="Paired-end reads" help="Select between paired and paired collection">

                <param name="nano" value="onp.fa"/>
            </conditional>
            <conditional name="pacbio_input">
                <param name="pb_input" value="No" />
            </conditional>
            <output name="superReads" ftype="fasta" />
        </test>
    </tests>
    <help><![CDATA[

        This implementation of MaSuRCA is for small projects that only have PE

1:86aa445e75d6

    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #set $long = 'false'
        #if $nanopore_input.np_input == "Yes":
            #if $pacbio_input.pb_input == "Yes":
                cat '$nanopore_input.nano' '$pacbio_input.pacbio' > \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
            #else:
                ln -s '$nanopore_input.nano' \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
            #end if
            #set $long = 'true'
        #elif $pacbio_input.pb_input == "Yes":
            ln -s '$pacbio_input.pacbio' \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
            #set $long = 'true'
        #end if
        masurca -t \${GALAXY_SLOTS:-8} -i
        #if str( $illumina_input.input_type ) == "single"
            '$illumina_input.fastq_input1'

            '$illumina_input.fastq_input1','$illumina_input.fastq_input2'
        #elif str( $illumina_input.input_type ) == "paired_collection"
            '$illumina_input.fastq_input1','$illumina_input.fastq_input2'
        #end if
        #if $long == "true":
            -r \$_GALAXY_JOB_TMP_DIR/long.fastq.gz
        #end if
    ]]></command>
    <inputs>
        <conditional name="illumina_input">
            <param name="input_type" type="select" label="Paired-end reads" help="Select between paired and paired collection">

                <param name="nano" value="onp.fa"/>
            </conditional>
            <conditional name="pacbio_input">
                <param name="pb_input" value="No" />
            </conditional>
            <output name="superReads" ftype="fasta">
                <assert_contents>
                    <has_line_matching expression="^TCCGAAAGTGTTAACTT.*"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

        This implementation of MaSuRCA is for small projects that only have PE