comparison macros.xml @ 10:910c6a1c3a27 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03

9:ed900cd4a0a9

<macros>
    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
    <token name="@TOOL_VERSION@">3.7.5</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">23.0</token>
    <token name="@USE_RANGE@">
        #if $use_range.select_use_range == "yes_use_range":
            --range $use_range.range_min:$use_range.range_max
        #end if

    <xml name="dpi">
        <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />
    </xml>

    <xml name="restrictionCutFile">
        <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only  mappable restriction sites. If given, the bins are set to match the restriction fragments
                (i.e. the region between one restriction site and the next)." />
    </xml>

    <xml name="restrictionSequence">
        <param argument="--restrictionSequence" type="text" optional="false" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
            &quot;dangling-ends&quot;. If not given, such statistics will not be available.">
            <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
        </param>
    </xml>
    <xml name="danglingSequence">
        <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting.
                    Each restriction enzyme recognizes a different DNA sequence and,

                    For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
                    For DpnII, the restriction site and dangling end sequence are the same: GATC.
                    This information is easily found on the description of the restriction enzyme.
                    The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
                    A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. ">
            <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
        </param>
    </xml>

    <xml name="zMax">
        <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" />

10:910c6a1c3a27

<macros>
    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
    <token name="@TOOL_VERSION@">3.7.5</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">23.0</token>
    <token name="@USE_RANGE@">
        #if $use_range.select_use_range == "yes_use_range":
            --range $use_range.range_min:$use_range.range_max
        #end if

    <xml name="dpi">
        <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />
    </xml>

    <xml name="restrictionCutFile">
        <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
                (i.e. the region between one restriction site and the next)." />
    </xml>

    <xml name="restrictionSequence">
        <param argument="--restrictionSequence" type="text" optional="false" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
            &quot;dangling-ends&quot;. If not given, such statistics will not be available.">
            <validator type="regex" message="Only space separated nucleotide sequences are allowed.">^(?:[ATCGatcg]+(?:\s[ATCGatcg]+)*)?$</validator>
        </param>
    </xml>
    <xml name="danglingSequence">
        <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting.
                    Each restriction enzyme recognizes a different DNA sequence and,

                    For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
                    For DpnII, the restriction site and dangling end sequence are the same: GATC.
                    This information is easily found on the description of the restriction enzyme.
                    The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
                    A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. ">
            <validator type="regex" message="Only space separated nucleotide sequences are allowed.">^(?:[ATCGatcg]+(?:\s[ATCGatcg]+)*)?$</validator>
        </param>
    </xml>

    <xml name="zMax">
        <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" />