Mercurial > repos > bgruening > pandas_rolling_window

annotate pandas_rolling.xml @ 0:e9af125ddb86 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
author bgruening
date Mon, 20 May 2019 08:42:28 -0400
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e9af125ddb86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
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1 <tool id="pandas_rolling_window" name="Rolling window" version="0.1">
e9af125ddb86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
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2 <description>over a dataframe (e.g. for data smoothing)</description>
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3 <requirements>
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4 <requirement type="package" version="1.16.3">numpy</requirement>
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5 <requirement type="package" version="1.2.1">scipy</requirement>
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6 <requirement type="package" version="0.24.2">pandas</requirement>
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7 </requirements>
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8 <command>
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9 <![CDATA[
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10
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11 cat '$pandas_script' &&
e9af125ddb86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
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12 python '$pandas_script'
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13
e9af125ddb86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
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14 ]]>
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15 </command>
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16 <configfiles>
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17 <configfile name="pandas_script"><![CDATA[
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18 import argparse
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19 import sys
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20
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21 import pandas as pd
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22
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23 kwargs = dict()
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24 window_type = '$smooth_function.smooth_function_opts_selector'
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25
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26 #if $smooth_function.smooth_function_opts_selector == 'gaussian':
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27 kwargs.update({'std': $smooth_function.gaussian_std})
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28 #elif $smooth_function.smooth_function_opts_selector == 'general_gaussian':
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29 kwargs = ({'power': $smooth_function.ggaussian_power, 'width': $smooth_function.ggaussian_width})
e9af125ddb86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
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30 #elif $smooth_function.smooth_function_opts_selector == 'kaiser':
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31 kwargs.update({'beta': $smooth_function.kaiser_beta})
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32 #elif $smooth_function.smooth_function_opts_selector == 'slepian':
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33 kwargs.update({'width': $smooth_function.slepian_width})
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34 #end if
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35
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36 df = pd.read_csv('${infile}', sep='\t', index_col=None, header=None, dtype={'strand': object} )
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37
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38 #if $group_column:
e9af125ddb86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
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39 df['aggregate'] = df.groupby( int($group_column)-1, sort=False )[int($value_column)-1].rolling(${window_len}, win_type=window_type, center=$centering ).${statistics}(**kwargs).reset_index(drop=True)
e9af125ddb86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
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40 #else:
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41 df['aggregate'] = df[int($value_column)-1].rolling(${window_len}, win_type=window_type, center=$centering ).${statistics}(**kwargs).reset_index(drop=True)
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42 #end if
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43
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44 df.to_csv('${outfile}', index=False, header=False, sep='\t', na_rep='0', float_format='%.2f')
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45 ]]> </configfile>
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46 </configfiles>
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47 <inputs>
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48 <param name="infile" type="data" format="tabular,bed.interval" label="Select input file in tabular or BED format"/>
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49 <param name="group_column" type="data_column" data_ref="infile" optional="true" label="Optional column to group"
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50 help="For example if you have a chromosome column you probably want to group each chromosome before you apply any function." />
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51
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52 <param name="value_column" type="data_column" data_ref="infile" label="Column with the value of interest"
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53 help="" />
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54
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55 <conditional name="smooth_function">
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56 <param name="smooth_function_opts_selector" type="select" label="Provide a window type"
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57 help="For more information please see https://en.wikipedia.org/wiki/Window_function">
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58 <option value="boxcar" selected="True">Boxcar or Dirichlet, all points are evenly weighted</option>
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59 <option value="triang">triang</option>
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60 <option value="blackman">blackman</option>
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61 <option value="hamming">hamming</option>
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62 <option value="bartlett">bartlett</option>
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63 <option value="parzen">parzen</option>
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64 <option value="bohman">bohman</option>
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65 <option value="blackmanharris">blackmanharris</option>
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66 <option value="nuttall">nuttall</option>
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67 <option value="barthann">barthann</option>
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68 <!--option value="kaiser">kaiser</option>
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69 <option value="gaussian">gaussian</option>
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70 <option value="general_gaussian">general gaussian</option>
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71 <option value="slepian">slepian</option-->
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72 </param>
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73 <when value="boxcar" />
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74 <when value="triang" />
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75 <when value="blackman" />
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76 <when value="hamming" />
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77 <when value="bartlett" />
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78 <when value="parzen" />
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79 <when value="bohman" />
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80 <when value="blackmanharris" />
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81 <when value="nuttall" />
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82 <when value="barthann" />
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83 <when value="kaiser">
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84 <param name="kaiser_beta" type="float" value="0.1" min='0.0' label="beta" />
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85 </when>
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86 <when value="gaussian">
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87 <param name="gaussian_std" type="float" value="0.1" min='0.0' label="std" />
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88 </when>
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89 <when value="general_gaussian">
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90 <param name="ggaussian_power" type="integer" value="2" min='1' label="power" />
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91 <param name="ggaussian_width" type="integer" value="2" min="1" label="width" />
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92 </when>
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93 <when value="slepian">
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94 <param name="slepian_width" type="integer" value="2" min="1" label="width" />
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95 </when>
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96 </conditional>
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97
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98 <param name="statistics" type="select" label="Provide a statistical function">
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99 <option value="count">Number of non-null observations (count)</option>
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100 <option value="sum">Sum of values (sum)</option>
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101 <option value="mean" selected="true">Mean of values (mean)</option>
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102 <option value="median">Arithmetic median of values (median)</option>
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103 <option value="min">Minimum (min)</option>
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104 <option value="max">max (max)</option>
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105 <option value="std">Bessel-corrected sample standard deviation (std)</option>
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106 <option value="var">Unbiased variance (var)</option>
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107 <option value="skew">Sample skewness (3rd moment)</option>
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108 <option value="kurt">Sample kurtosis (4th moment)</option>
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109 <option value="quantil">Sample quantile (value at %)</option>
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110 <option value="cov">Unbiased covariance (binary) (cov)</option>
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111 <option value="corr">Correlation (corr)</option>
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112 </param>
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113
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114 <param name="centering" type="boolean" truevalue="True" falsevalue="False" label="center smoothed values"
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115 help="By default the labels are set to the right edge of the window. Here you can change that to the center." />
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116 <!-- Options for all formats.-->
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117 <param name="window_len" type="integer" value="3" min="2" label="Window length"/>
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118 </inputs>
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119 <outputs>
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120 <data name="outfile" format_source="infile" />
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121 </outputs>
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122 <tests>
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123 <test>
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124 <param name="infile" value="1.bedgraph"/>
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125 <param name="group_column" value="1"/>
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126 <param name="value_column" value="5"/>
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127 <conditional name="smooth_function">
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128 <param name="smooth_function_opts_selector" value="boxcar"/>
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129 </conditional>
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130 <param name="window_len" value="3"/>
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131 <output name="outfile" value="1_boxcar.bedgraph"/>
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132 </test>
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133 <test>
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134 <!-- None test -->
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135 <param name="infile" value="1.bedgraph"/>
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136 <param name="value_column" value="5"/>
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137 <conditional name="smooth_function">
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138 <param name="smooth_function_opts_selector" value="boxcar"/>
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139 </conditional>
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140 <param name="window_len" value="3"/>
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141 <output name="outfile" value="2_boxcar.bedgraph"/>
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142 </test>
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143 <test>
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144 <param name="infile" value="1.bedgraph"/>
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145 <param name="group_column" value="1"/>
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146 <param name="value_column" value="5"/>
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147 <conditional name="smooth_function">
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148 <param name="smooth_function_opts_selector" value="hamming"/>
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149 </conditional>
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150 <param name="window_len" value="3"/>
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151 <param name="statistics" value="sum"/>
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152 <output name="outfile" value="1_hamming.bedgraph"/>
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153 </test>
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154 <test>
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155 <param name="infile" value="1.bedgraph"/>
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156 <param name="value_column" value="5"/>
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157 <conditional name="smooth_function">
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158 <param name="smooth_function_opts_selector" value="hamming"/>
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159 </conditional>
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160 <param name="window_len" value="3"/>
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161 <param name="statistics" value="sum"/>
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162 <output name="outfile" value="2_hamming.bedgraph"/>
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163 </test>
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164 </tests>
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165 <help>
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166 <![CDATA[
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167
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168 **What it does**
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169
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170 Provides rolling window calculations, e.g. for smoothing values.
e9af125ddb86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
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171
e9af125ddb86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
bgruening
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172
e9af125ddb86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
bgruening
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173 ]]>
e9af125ddb86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
bgruening
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174 </help>
e9af125ddb86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window commit bdbedf42854d16bb00c396045007d4baece0a869
bgruening
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175 </tool>