comparison mummer.xml @ 5:57f042937ba7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538

4:bcd65de9725b

    <expand macro="requirements">
        <expand macro="gnuplot_requirement"/>
    </expand>
    <command detect_errors="exit_code">
        <![CDATA[
        mummer 
            $anchoring
            -l '$min'
            $direction
            $force
            $chars

                </param>
                <param name="child" type="select" label="Child" help="Use child table in the index and during search? (-child)" >
                    <option value="0">No</option>
                    <option value="1">Yes</option>
                </param>
                <param name="skip" type="integer" argument="-skip" value="10" label="Sparsify"
                    help="Sparsify the MEM-finding algorithm even more, performing jumps of skip*k [auto (l-10)/k]. (-skip)" />
                <param name="kmer" type="integer" argument="-kmer" value="1" label="kmer Table"
                    help="Use kmer table containing sa-intervals (speeds up searching first k characters) in the index and during search. (-kmer)" />
            </when>
            <when value="defaults" />
        </conditional>
        <conditional name="mumplot" >

        <data name="png_output" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" >
            <filter>mumplot['plot'] == 'yes'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
            <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
            <param name="options|advanced" value="defaults" />
            <param name="plot" value="yes" />
            <output name="output" ftype="tabular" compare="diff" value="mummer.txt" />

**Options:**::

    mummer

    -mumreference    Compute maximal matches that are unique in the reference- sequence but not 
                     necessarily in the query-sequence (default)

    -maxmatch        Compute all maximal matches regardless of their uniqueness

    -l               Set the minimum length of a match

    -c               Report the query position of a reverse complement match
                     relative to the forward strand of the query sequence

    mummerplot

    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest 
                   sequence end

    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default 
                   color by match dir) If the plot is very sparse, edit the .gp script to plot with 
                   'linespoints' instead of 'lines'

    -c             Generate a reference coverage plot (default for .tiling)

    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on 
                   either sequence, i.e. a one-to-one mapping of reference and query subsequences

    --fat          Layout sequences using fattest alignment only

    -IdR           Plot a particular reference sequence ID on the X-axis

5:57f042937ba7

    <expand macro="requirements">
        <expand macro="gnuplot_requirement"/>
    </expand>
    <command detect_errors="exit_code">
        <![CDATA[
        mummer
            $anchoring
            -l '$min'
            $direction
            $force
            $chars

                </param>
                <param name="child" type="select" label="Child" help="Use child table in the index and during search? (-child)" >
                    <option value="0">No</option>
                    <option value="1">Yes</option>
                </param>
                <param  type="integer" argument="-skip" value="10" label="Sparsify"
                    help="Sparsify the MEM-finding algorithm even more, performing jumps of skip*k [auto (l-10)/k]. (-skip)" />
                <param  type="integer" argument="-kmer" value="1" label="kmer Table"
                    help="Use kmer table containing sa-intervals (speeds up searching first k characters) in the index and during search. (-kmer)" />
            </when>
            <when value="defaults" />
        </conditional>
        <conditional name="mumplot" >

        <data name="png_output" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" >
            <filter>mumplot['plot'] == 'yes'</filter>
        </data>
    </outputs>
    <tests>
        <test  expect_num_outputs="2">
            <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
            <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
            <param name="options|advanced" value="defaults" />
            <param name="plot" value="yes" />
            <output name="output" ftype="tabular" compare="diff" value="mummer.txt" />

**Options:**::

    mummer

    -mumreference    Compute maximal matches that are unique in the reference- sequence but not
                     necessarily in the query-sequence (default)

    -maxmatch        Compute all maximal matches regardless of their uniqueness

    -l               Set the minimum length of a match

    -c               Report the query position of a reverse complement match
                     relative to the forward strand of the query sequence

    mummerplot

    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
                   sequence end

    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default
                   color by match dir) If the plot is very sparse, edit the .gp script to plot with
                   'linespoints' instead of 'lines'

    -c             Generate a reference coverage plot (default for .tiling)

    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on
                   either sequence, i.e. a one-to-one mapping of reference and query subsequences

    --fat          Layout sequences using fattest alignment only

    -IdR           Plot a particular reference sequence ID on the X-axis