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comparison macros.xml @ 0:a3d8cadaf060 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/statistics commit 7c5002672919ca1e5eacacb835a4ce66ffa19656
author bgruening
date Mon, 21 Nov 2022 18:07:45 +0000
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1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="1.23.5">numpy</requirement>
5 <requirement type="package" version="1.9.3">scipy</requirement>
6 </requirements>
7 </xml>
8 <xml name="macro_sample_one_cols">
9 <param name="sample_one_cols" multiple="True" type="data_column" data_ref="infile" label="Column for sample one"/>
10 </xml>
11 <xml name="macro_sample_two_cols">
12 <param name="sample_two_cols" multiple="True" type="data_column" data_ref="infile" optional="True" label="Column for sample two"/>
13 </xml>
14 <xml name="macro_sample_cols_min2">
15 <repeat name="samples" title="more samples" min='2'>
16 <param name="sample_cols" multiple="True" type="data_column" data_ref="infile" label="Column for sample"/>
17 </repeat>
18 </xml>
19 <xml name="macro_sample_cols_min3">
20 <repeat name="samples" title="more samples" min='3'>
21 <param name="sample_cols" multiple="True" type="data_column" data_ref="infile" label="Column for sample"/>
22 </repeat>
23 </xml>
24 <xml name="macro_zero_method">
25 <param name="zero_method" type="select" label="pratt,wilcox,zsplit">
26 <option value="pratt">Pratt treatment: includes zero-differences in the ranking process</option>
27 <option value="wilcox">Wilcox treatment: discards all zero-differences</option>
28 <option value="zsplit">Zero rank split: just like Pratt, but spliting the zero rank between positive and negative ones</option>
29 </param>
30 </xml>
31 <xml name="macro_center">
32 <param name="center" type="select" label="Which function of the data to use in the test ">
33 <option value="median">median</option>
34 <option value="mean">mean</option>
35 <option value="trimmed">trimmed</option>
36 </param>
37 </xml>
38 <xml name="macro_interpolation">
39 <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">
40 <option value="fraction">fraction</option>
41 <option value="lower">lower</option>
42 <option value="higher">higher</option>
43 </param>
44 </xml>
45 <xml name="macro_ties">
46 <param name="ties" type="select" label="Determines how values equal to the grand median are classified in the contingency table">
47 <option value="below">below</option>
48 <option value="above">above</option>
49 <option value="ignore">ignore</option>
50 </param>
51 </xml>
52 <xml name="macro_method">
53 <param name="method" type="select" label="Maximizes the Pearson correlation coefficient">
54 <option value="pearsonr">pearsonr</option>
55 <option value="mle">mle</option>
56 <option value="all">all</option>
57 </param>
58 </xml>
59 <xml name="macro_dist">
60 <param name="dist" type="select" label="the type of distribution to test against. The default is ‘norm’ and ‘extreme1’ is a synonym for ‘gumbel’">
61 <option value="norm">norm</option>
62 <option value="expon">expon</option>
63 <option value="logistic">logistic</option>
64 <option value="gumbel">gumbel</option>
65 <option value="extreme1">extreme1</option>
66 </param>
67 </xml>
68 <xml name="macro_tail">
69 <param name="tail" type="select" label="From which tail">
70 <option value="right">right</option>
71 <option value="left">left</option>
72 </param>
73 </xml>
74 <xml name="macro_kind">
75 <param name="kind" type="select" label="This optional parameter specifies the interpretation of the resulting score">
76 <option value="rank">rank</option>
77 <option value="weak">weak</option>
78 <option value="strict">strict</option>
79 <option value="mean">mean</option>
80 </param>
81 </xml>
82 <xml name="macro_md">
83 <param name="md" type="select" label="The method used to assign ranks to tied elements">
84 <option value="average">average</option>
85 <option value="min">min</option>
86 <option value="max">max</option>
87 <option value="dense">dense</option>
88 <option value="ordinal">ordinal</option>
89 </param>
90 </xml>
91 <xml name="macro_statistic">
92 <param name="statistic" type="select" label="The statistic to compute ">
93 <option value="mean">mean</option>
94 <option value="median">median</option>
95 <option value="count">count</option>
96 <option value="sum">sum</option>
97 </param>
98 </xml>
99 <xml name="macro_alternative">
100 <param name="alternative" type="select" label="Defines the alternative hypothesis">
101 <option value="two-sided">two-sided</option>
102 <option value="less">less</option>
103 <option value="greater">greater</option>
104 </param>
105 </xml>
106 <xml name="macro_mode">
107 <param name="mode" type="select" label="Defines the distribution used for calculating the p-value">
108 <option value="approx">approx</option>
109 <option value="asymp">asymp</option>
110 </param>
111 </xml>
112 <xml name="macro_interpolation">
113 <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">
114 <option value="fraction">fraction</option>
115 <option value="lower">lower</option>
116 <option value="higher">higher</option>
117 </param>
118 </xml>
119 <xml name="macro_correction">
120 <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."/>
121 </xml>
122 <xml name="macro_printextras">
123 <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" />
124 </xml>
125 <xml name="macro_initial_lexsort">
126 <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"/>
127 </xml>
128 <xml name="macro_cdf">
129 <param name="cdf" type="text" value="norm" label="If a string, it should be the name of a distribution in scipy.stats"/>
130 </xml>
131 <xml name="macro_ni">
132 <param name="ni" type="integer" value="20" label="N" optional="True" help="Sample size if rvs is string or callable."/>
133 </xml>
134 <xml name="macro_mwu_use_continuity">
135 <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" />
136 </xml>
137 <xml name="macro_equal_var">
138 <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" />
139 </xml>
140 <xml name="macro_base">
141 <param name="base" type="float" value="1.6" label="base" help="The logarithmic base to use, defaults to e"/>
142 </xml>
143 <xml name="macro_med">
144 <param name="med" type="text" value="fisher" label="Name of method to use to combine p-values"/>
145 </xml>
146 <xml name="macro_reta">
147 <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"/>
148 </xml>
149 <xml name="macro_n_in">
150 <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"/>
151 </xml>
152 <xml name="macro_n_moment">
153 <param name="n" type="integer" value="1" label="moment" help="order of central moment that is returned"/>
154 </xml>
155 <xml name="macro_equal_var">
156 <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" />
157 </xml>
158 <xml name="macro_imbda">
159 <param name="imbda" type="float" value="" label="imbda" optional="True" help="do the transformation for that value"/>
160 </xml>
161 <xml name="macro_ddof">
162 <param name="ddof" type="integer" value="0" label="ddof" optional="True" help="Degrees of freedom correction for standard deviation. "/>
163 </xml>
164 <xml name="macro_dtype">
165 <param name="dtype" type="text" value="" optional="True" label="Type of the returned array and of the accumulator in which the elements are summed"/>
166 </xml>
167 <xml name="macro_m">
168 <param name="m" type="float" value="4" label="low" help="Lower bound factor of sigma clipping. Default is 4."/>
169 </xml>
170 <xml name="macro_mf">
171 <param name="mf" type="float" value="" label="lower_limit" optional="True" help="lower values for the range of the histogram"/>
172 </xml>
173 <xml name="macro_nf">
174 <param name="nf" type="float" value="" label="upper_limit" optional="True" help="higher values for the range of the histogram"/>
175 </xml>
176 <xml name="macro_b">
177 <param name="b" type="integer" value="10" label="numbins" help="The number of bins to use for the histogram"/>
178 </xml>
179 <xml name="macro_proportiontocut">
180 <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"/>
181 </xml>
182 <xml name="macro_alpha">
183 <param name="alpha" type="float" value="0.9" label="alpha" optional="True" help="Probability that the returned confidence interval contains the true parameter"/>
184 </xml>
185 <xml name="macro_score">
186 <param name="score" type="integer" value="0" label="score" optional="True" help="Score that is compared to the elements in a"/>
187 </xml>
188 <xml name="macro_axis">
189 <param name="axis" type="integer" value="0" label="0 means one-dimensional array" help="Axis along which the kurtosis is calculated"/>
190 </xml>
191 <xml name="macro_new">
192 <param name="new" type="float" value="0" label="newval" help="Value to put in place of values in a outside of bounds"/>
193 </xml>
194 <xml name="macro_fisher">
195 <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)." />
196 </xml>
197 <xml name="macro_b">
198 <param name="b" type="integer" value="10" label="numbins" help="The number of bins to use for the histogram"/>
199 </xml>
200 <xml name="macro_proportiontocut">
201 <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"/>
202 </xml>
203 <xml name="macro_bias">
204 <param name="bias" type="boolean" truevalue="--bias" falsevalue="" checked="true" label="bias" help="If False, then the calculations are corrected for statistical bias." />
205 </xml>
206 <xml name="macro_lambda_">
207 <param name="lambda_" type="float" value="1" label="lambda_" optional="True" help="lambda_ gives the power in the Cressie-Read power divergence statistic."/>
208 </xml>
209 <xml name="macro_inclusive">
210 <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" />
211 </xml>
212 <xml name="macro_p">
213 <param name="p" type="float" value="0.5" />
214 </xml>
215 <xml name="macro_inclusive1">
216 <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" />
217 </xml>
218 <xml name="macro_inclusive2">
219 <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" />
220 </xml>
221 <xml name="macro_inclusive">
222 <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" />
223 </xml>
224 </macros>