annotate macros.xml @ 0:178b22349b79 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/statistics commit 7c5002672919ca1e5eacacb835a4ce66ffa19656

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.23.5">numpy</requirement>
            <requirement type="package" version="1.9.3">scipy</requirement>
        </requirements>
    </xml>
    <xml name="macro_sample_one_cols">
        <param name="sample_one_cols" multiple="True" type="data_column" data_ref="infile" label="Column for sample one"/>
    </xml>
    <xml name="macro_sample_two_cols">
        <param name="sample_two_cols" multiple="True" type="data_column" data_ref="infile" optional="True" label="Column for sample two"/>
    </xml>
    <xml name="macro_sample_cols_min2">
        <repeat name="samples" title="more samples" min='2'>
            <param name="sample_cols" multiple="True" type="data_column" data_ref="infile" label="Column for sample"/>
        </repeat>
    </xml>
    <xml name="macro_sample_cols_min3">
        <repeat name="samples" title="more samples" min='3'>
            <param name="sample_cols" multiple="True" type="data_column" data_ref="infile" label="Column for sample"/>
        </repeat>
    </xml>
    <xml name="macro_zero_method">
        <param name="zero_method" type="select" label="pratt,wilcox,zsplit">
            <option value="pratt">Pratt treatment: includes zero-differences in the ranking process</option>
            <option value="wilcox">Wilcox treatment: discards all zero-differences</option>
            <option value="zsplit">Zero rank split: just like Pratt, but spliting the zero rank between positive and negative ones</option>
        </param>
    </xml>
    <xml name="macro_center">
        <param name="center" type="select" label="Which function of the data to use in the test ">
            <option value="median">median</option>
            <option value="mean">mean</option>
            <option value="trimmed">trimmed</option>
        </param>
    </xml>
    <xml name="macro_interpolation">
        <param name="interpolation" type="select" label="this specifies the interpolation method to use, when the desired quantile lies between two data points i and j">
            <option value="fraction">fraction</option>
            <option value="lower">lower</option>
            <option value="higher">higher</option>
        </param>
    </xml>
    <xml name="macro_ties">
        <param name="ties" type="select" label="Determines how values equal to the grand median are classified in the contingency table">
        <option value="below">below</option>
        <option value="above">above</option>
        <option value="ignore">ignore</option>
        </param>
    </xml>
    <xml name="macro_method">
        <param name="method" type="select" label="Maximizes the Pearson correlation coefficient">
        <option value="pearsonr">pearsonr</option>
        <option value="mle">mle</option>
            <option value="all">all</option>
        </param>
    </xml>
    <xml name="macro_dist">
        <param name="dist" type="select" label="the type of distribution to test against. The default is ‘norm’ and ‘extreme1’ is a synonym for ‘gumbel’">
            <option value="norm">norm</option>
            <option value="expon">expon</option>
            <option value="logistic">logistic</option>
            <option value="gumbel">gumbel</option>
            <option value="extreme1">extreme1</option>
        </param>
    </xml>
    <xml name="macro_tail">
        <param name="tail" type="select" label="From which tail">
            <option value="right">right</option>
            <option value="left">left</option>
        </param>
    </xml>
    <xml name="macro_kind">
        <param name="kind" type="select" label="This optional parameter specifies the interpretation of the resulting score">
            <option value="rank">rank</option>
            <option value="weak">weak</option>
            <option value="strict">strict</option>
            <option value="mean">mean</option>
        </param>
    </xml>
    <xml name="macro_md">
        <param name="md" type="select" label="The method used to assign ranks to tied elements">
            <option value="average">average</option>
            <option value="min">min</option>
            <option value="max">max</option>
            <option value="dense">dense</option>
            <option value="ordinal">ordinal</option>
        </param>
    </xml>
    <xml name="macro_statistic">
        <param name="statistic" type="select" label="The statistic to compute ">
            <option value="mean">mean</option>
            <option value="median">median</option>
            <option value="count">count</option>
            <option value="sum">sum</option>
        </param>
    </xml>
    <xml name="macro_alternative">
        <param name="alternative" type="select" label="Defines the alternative hypothesis">
            <option value="two-sided">two-sided</option>
            <option value="less">less</option>
            <option value="greater">greater</option>
        </param>
    </xml>
    <xml name="macro_mode">
        <param name="mode" type="select" label="Defines the distribution used for calculating the p-value">
            <option value="approx">approx</option>
            <option value="asymp">asymp</option>
        </param>
    </xml>
    <xml name="macro_interpolation">
        <param name="interpolation" type="select" label="this specifies the interpolation method to use, when the desired quantile lies between two data points i and j">
            <option value="fraction">fraction</option>
            <option value="lower">lower</option>
            <option value="higher">higher</option>
        </param>
    </xml>
    <xml name="macro_correction">
        <param name="correction" type="boolean" truevalue="--correction" falsevalue="" checked="True" label="If True, and the degrees of freedom is 1, apply Yates’ correction for continuity."/>
    </xml>
    <xml name="macro_printextras">
        <param name="printextras" type="boolean" truevalue="--printextras" falsevalue="" checked="False" label="printextras" help="If True, if there are extra points a warning is raised saying how many of those points there are" />
    </xml>
    <xml name="macro_initial_lexsort">
        <param name="initial_lexsort" type="boolean" truevalue="--initial_lexsort" falsevalue="" checked="True" label="Whether to use lexsort or quicksort as the sorting method for the initial sort of the inputs"/>
    </xml>
    <xml name="macro_cdf">
        <param name="cdf" type="text" value="norm" label="If a string, it should be the name of a distribution in scipy.stats"/>
    </xml>
    <xml name="macro_ni">
        <param name="ni" type="integer" value="20" label="N" optional="True" help="Sample size if rvs is string or callable."/>
    </xml>
    <xml name="macro_mwu_use_continuity">
        <param name="mwu_use_continuity" type="boolean" label="Enable continuity correction" help="Whether a continuity correction (1/2.) should be taken into account." truevalue="--mwu_use_continuity" falsevalue="" checked="true" />
    </xml>
    <xml name="macro_equal_var">
        <param name="equal_var" type="boolean" label="assume equal population" help="If set perform a standard independent 2 sample test that assumes equal population variances. If not set, perform Welch’s t-test, which does not assume equal population variance." truevalue="--equal_var" falsevalue="" checked="true" />
    </xml>
    <xml name="macro_base">
        <param name="base" type="float" value="1.6" label="base" help="The logarithmic base to use, defaults to e"/>
    </xml>
    <xml name="macro_med">
        <param name="med" type="text" value="fisher" label="Name of method to use to combine p-values"/>
    </xml>
    <xml name="macro_reta">
        <param name="reta" type="boolean" truevalue="--reta" falsevalue="" checked="False" label="Whether or not to return the internally computed a values." help="Whether or not to return the internally computed a values"/>
    </xml>
    <xml name="macro_n_in">
        <param name="n" type="integer" value="1" label="the number of trials" help="This is ignored if x gives both the number of successes and failures"/>
    </xml>
    <xml name="macro_n_moment">
        <param name="n" type="integer" value="1" label="moment"  help="order of central moment that is returned"/>
    </xml>
    <xml name="macro_equal_var">
        <param name="equal_var" type="boolean" label="assume equal population" help="If set perform a standard independent 2 sample test that assumes equal population variances. If not set, perform Welch’s t-test, which does not assume equal population variance." truevalue="--equal_var" falsevalue="" checked="true" />
    </xml>
    <xml name="macro_imbda">
        <param name="imbda" type="float" value="" label="imbda" optional="True" help="do the transformation for that value"/>
    </xml>
    <xml name="macro_ddof">
        <param name="ddof" type="integer" value="0" label="ddof" optional="True" help="Degrees of freedom correction for standard deviation. "/>
    </xml>
    <xml name="macro_dtype">
        <param name="dtype" type="text" value="" optional="True" label="Type of the returned array and of the accumulator in which the elements are summed"/>
    </xml>
    <xml name="macro_m">
        <param name="m" type="float" value="4" label="low" help="Lower bound factor of sigma clipping. Default is 4."/>
    </xml>
    <xml name="macro_mf">
        <param name="mf" type="float" value="" label="lower_limit" optional="True" help="lower values for the range of the histogram"/>
    </xml>
    <xml name="macro_nf">
        <param name="nf" type="float" value="" label="upper_limit" optional="True" help="higher values for the range of the histogram"/>
    </xml>
    <xml name="macro_b">
        <param name="b" type="integer" value="10" label="numbins" help="The number of bins to use for the histogram"/>
    </xml>
    <xml name="macro_proportiontocut">
        <param name="proportiontocut" type="float" value="0.05" label="proportiontocut" optional="True" help="Proportion (in range 0-1) of total data set to trim of each end"/>
    </xml>
    <xml name="macro_alpha">
        <param name="alpha" type="float" value="0.9" label="alpha" optional="True" help="Probability that the returned confidence interval contains the true parameter"/>
    </xml>
    <xml name="macro_score">
        <param name="score" type="integer" value="0" label="score" optional="True" help="Score that is compared to the elements in a"/>
    </xml>
    <xml name="macro_axis">
        <param name="axis" type="integer" value="0" label="0 means one-dimensional array" help="Axis along which the kurtosis is calculated"/>
    </xml>
    <xml name="macro_new">
        <param name="new" type="float" value="0" label="newval" help="Value to put in place of values in a outside of bounds"/>
    </xml>
    <xml name="macro_fisher">
        <param name="fisher" type="boolean" truevalue="--fisher" falsevalue="" checked="true" label="Fisher’s definition is used" help="If True, Fisher’s definition is used (normal ==> 0.0). If False, Pearson’s definition is used (normal ==> 3.0)." />
    </xml>
    <xml name="macro_b">
        <param name="b" type="integer" value="10" label="numbins" help="The number of bins to use for the histogram"/>
    </xml>
    <xml name="macro_proportiontocut">
        <param name="proportiontocut" type="float" value="0.05" label="proportiontocut" optional="True" help="Proportion (in range 0-1) of total data set to trim of each end"/>
    </xml>
    <xml name="macro_bias">
        <param name="bias" type="boolean" truevalue="--bias" falsevalue="" checked="true" label="bias" help="If False, then the calculations are corrected for statistical bias." />
    </xml>
    <xml name="macro_lambda_">
        <param name="lambda_" type="float" value="1" label="lambda_" optional="True" help="lambda_ gives the power in the Cressie-Read power divergence statistic."/>
    </xml>
    <xml name="macro_inclusive">
        <param name="inclusive" type="boolean" truevalue="--inclusive" falsevalue="" checked="true" label="flag" help="These flags determine whether values exactly equal to the lower or upper limits are included" />
    </xml>
    <xml name="macro_p">
        <param name="p" type="float" value="0.5" />
    </xml>
    <xml name="macro_inclusive1">
        <param name="inclusive1" type="boolean" truevalue="--inclusive1" falsevalue="" checked="true" label="lower flag" help="These flags determine whether values exactly equal to the lower or upper limits are included" />
    </xml>
    <xml name="macro_inclusive2">
        <param name="inclusive2" type="boolean" truevalue="--inclusive2" falsevalue="" checked="true" label="upper flag" help="These flags determine whether values exactly equal to the lower or upper limits are included" />
    </xml>
    <xml name="macro_inclusive">
        <param name="inclusive" type="boolean" truevalue="--inclusive" falsevalue="" checked="true" label="flag" help="These flags determine whether values exactly equal to the lower or upper limits are included" />
    </xml>
</macros>