Mercurial > repos > iuc > datamash_ops

annotate datamash-ops.xml @ 8:f11dedb74b83 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
author iuc
date Sun, 10 Apr 2022 11:39:33 +0000
parents 0ea09f02e2e5
children 4b7dd5ff6497
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f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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1 <tool id="datamash_ops" name="Datamash" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>(operations on tabular data)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 datamash
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11 $header_in
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12 $header_out
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13 $need_sort
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14 $print_full_line
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15 $ignore_case
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f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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16 @FIELD_SEPARATOR@
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17 #if str($grouping) != ''
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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18 --group '$grouping'
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19 #end if
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20 #for $oper in $operations
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21 ${oper.op_name}
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22 ${oper.op_column}
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23 #end for
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24 < $in_file > '$out_file'
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25 ]]>
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26 </command>
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27 <expand macro="inputs_outputs">
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28 <param argument="--group" name="grouping" type="text" label="Group by fields" help="Group consecutive rows with equal values in the chosen fields. If no columns are specified, each operation is performed in the entire input file. Comma separated list of column indices, e.g. 1,5">
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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29 <sanitizer invalid_char="">
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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30 <valid initial="string.digits">
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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31 <add value="," />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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32 </valid>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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33 <mapping initial="none">
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34 <add source=" " target=""/>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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35 </mapping>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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36 </sanitizer>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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37 <validator message="Invalid value in field. Allowed is a comma separated list of integer values or the empty string" type="regex">(^$)|(^\s*\d+\s*(,\s*\d+\s*)*$)</validator>
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38 </param>
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39 <param argument="--sort" name="need_sort" type="boolean" truevalue="--sort" falsevalue="" label="Sort input" help="Input file must be sorted by the grouping columns. Enable this option to automatically sort the input."/>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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40 <param argument="--header-in" type="boolean" truevalue="--header-in" falsevalue="" label="Input file has a header line" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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41 <param argument="--header-out" type="boolean" truevalue="--header-out" falsevalue="" label="Print header line" />
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42 <param argument="--full" name="print_full_line" type="boolean" truevalue="--full" falsevalue="" label="Print all fields from input file" />
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43 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" label="Ignore case when grouping" />
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44 <repeat name="operations" default="1" min="1" title="Operation to perform on each group">
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45 <param name="op_name" type="select" label="Type">
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46 <option value="count">count</option>
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47 <option value="sum">sum</option>
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48 <option value="min">minimum</option>
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49 <option value="max">maximum</option>
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50 <option value="absmin">Absolute minimum</option>
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51 <option value="absmax">Absolute maximum</option>
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52 <option value="mean">Mean</option>
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53 <option value="pstdev">Population Standard deviantion</option>
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54 <option value="sstdev">Sample Standard deviantion</option>
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55 <option value="median">Median</option>
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56 <option value="q1">1st quartile</option>
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57 <option value="q3">3rd quartile</option>
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58 <option value="iqr">Inter-quartile range</option>
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59 <option value="mad">Median Absolute Deviation</option>
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60 <option value="pvar">Variance (population)</option>
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61 <option value="svar">Variance (sample)</option>
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62 <option value="sskew">Skewness (sample)</option>
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63 <option value="pskew">Skewness (population)</option>
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64 <option value="skurt">Kurtosis (sample)</option>
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65 <option value="pkurt">Kurtosis (population)</option>
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66 <option value="jarque">Jarque-Bera Normality test</option>
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67 <option value="dpo">D Agostino-Pearson Omnibus Normality Test</option>
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68 <option value="mode">Mode</option>
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69 <option value="antimode">Anti-Mode</option>
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70 <option value="rand">One random value from the group</option>
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71 <option value="unique">Combine all unique values</option>
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72 <option value="collapse">Combine all values</option>
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73 <option value="countunique">Count Unique values</option>
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74 </param>
4
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75 <param name="op_column" data_ref="in_file" label="On column" type="data_column" />
0
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76 </repeat>
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77 </expand>
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78 <tests>
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79 <test>
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80 <param name="in_file" value="group_compute_input.txt" ftype="tabular" />
0
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81 <param name="grouping" value="2" />
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82 <param name="header_in" value="true" />
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83 <param name="header_out" value="true" />
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84 <param name="need_sort" value="true" />
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85 <param name="print_full_line" value="false" />
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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86 <param name="ignore_case" value="false" />
4
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87 <repeat name="operations">
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88 <param name="op_name" value="sum" />
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89 <param name="op_column" value="3" />
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90 </repeat>
5
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91 <output file="group_compute_output.txt" name="out_file" ftype="tabular" />
0
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92 </test>
8
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93 <test>
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94 <param name="in_file" value="group_compute_input.txt" ftype="tsv" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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95 <param name="grouping" value="2" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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96 <param name="header_in" value="true" />
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97 <param name="header_out" value="true" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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98 <param name="need_sort" value="true" />
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99 <param name="print_full_line" value="false" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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100 <param name="ignore_case" value="false" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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101 <repeat name="operations">
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102 <param name="op_name" value="sum" />
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103 <param name="op_column" value="3" />
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104 </repeat>
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105 <output file="group_compute_output.txt" name="out_file" ftype="tsv" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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106 </test>
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107 <test>
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108 <param name="in_file" value="group_compute_input.csv" ftype="csv" />
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109 <param name="grouping" value="2" />
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110 <param name="header_in" value="true" />
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111 <param name="header_out" value="true" />
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112 <param name="need_sort" value="true" />
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113 <param name="print_full_line" value="false" />
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114 <param name="ignore_case" value="false" />
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115 <repeat name="operations">
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116 <param name="op_name" value="sum" />
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117 <param name="op_column" value="3" />
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118 </repeat>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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119 <output name="out_file" ftype="csv">
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120 <assert_contents>
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121 <has_n_lines n="7"/>
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122 <has_line line="Arts,1310"/>
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123 </assert_contents>
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124 </output>
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125 </test>
0
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126 </tests>
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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127 <help>
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128 <![CDATA[
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129 @HELP_HEADER@
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130
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131 **Syntax**
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132
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133 This tools performs common operations (such as summing, counting, mean, standard-deviation) on input file, based on tabular data. The tool can also optionaly group the input based on a given field.
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134
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135 -----
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136
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137 **Example 1**
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138
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139 - Find the average score in statistics course of college students, grouped by their college major. The input file has three fields (Name,Major,Score) and a header line::
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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140
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141 Name Major Score
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142 Bryan Arts 68
8
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143 Gabriel Health-Medicine 100
0
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144 Isaiah Arts 80
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145 Tysza Business 92
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146 Zackery Engineering 54
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147 ...
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148 ...
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149
8
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150 - Grouping the input by the second column (*Major*), sorting the input, and performing operations **mean** and **sample standard deviation** on the third column (*Score*), gives::
0
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151
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152 GroupBy(Major) mean(Score) sstdev(Score)
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153 Arts 68.9474 10.4215
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154 Business 87.3636 5.18214
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155 Engineering 66.5385 19.8814
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156 Health-Medicine 90.6154 9.22441
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157 Life-Sciences 55.3333 20.606
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158 Social-Sciences 60.2667 17.2273
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159
8
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160 Note that input needs sorting here, since the column used for grouping (*Major*) is not sorted.
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161
0
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162 This sample file is available at http://www.gnu.org/software/datamash .
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163
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164 **Example 2**
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165
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166 - Using the UCSC RefSeq Human Gene Track, available at: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz
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167
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168 - List the number and identifiers of isoforms per gene. The gene identifier is in column 13, the isoform/transcript identifier is in column 2. Grouping by column 13 and performing **count** and **Combine all values** on column 2, gives::
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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169
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170 GroupBy(field-13) count(field-2) collapse(field-2)
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171 A1BG 1 NM_130786
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172 A1BG-AS1 1 NR_015380
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173 A1CF 6 NM_001198818,NM_001198819,NM_001198820,NM_014576,NM_138932,NM_138933
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174 A2M 1 NM_000014
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175 A2M-AS1 1 NR_026971
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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176 A2ML1 2 NM_001282424,NM_144670
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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177 ...
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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178
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179 - Count how many transcripts are listed for each chromosome and strand. Chromosome is on column 3, Strand is in column 4. Transcript identifiers are in column 2. Grouping by columns **3,4** and performing operation **count** on column 2, gives::
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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180
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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181 GroupBy(field-3) GroupBy(field-4) count(field-2)
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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182 chr1 + 2456
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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183 chr1 - 2431
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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184 chr2 + 1599
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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185 chr2 - 1419
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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186 chr3 + 1287
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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187 chr3 - 1249
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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188 ...
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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189
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190 @HELP_FOOTER@
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191 ]]>
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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192 </help>
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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193 </tool>