Mercurial > repos > iuc > datamash_ops

annotate datamash-ops.xml @ 1:2f3c6f2dcf39 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
author iuc
date Wed, 21 Sep 2016 21:44:29 -0400
parents c4611129661b
children 562f3c677828
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c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
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1 <?xml version="1.0"?>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
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2 <tool id="datamash_ops" name="Datamash" version="1.0.6">
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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3 <description>(operations on tabular data)</description>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
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4 <macros>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
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5 <import>macros.xml</import>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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6 </macros>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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7 <expand macro="requirements" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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8 <expand macro="stdio" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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9 <command>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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10 <![CDATA[
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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11 datamash
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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12 $header_in
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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13 $header_out
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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14 $need_sort
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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15 $print_full_line
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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16 $ignore_case
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17 #if str($grouping).strip()
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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18 --group '$grouping'
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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19 #end if
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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20 #for $oper in $operations
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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21 ${oper.op_name}
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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22 ${oper.op_column}
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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23 #end for
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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24 < $in_file > $out_file
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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25 ]]>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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26 </command>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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27 <expand macro="inputs_outputs">
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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28 <param help="Example: to group by the first and fourth fields, use 1,4." label="Group by fields" name="grouping" type="text">
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
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29 <validator message="Invalid value in field. Allowed values are 0-9, space, comma." type="regex">^[0-9, ]*$</validator>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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30 </param>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
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31 <param falsevalue="" help="--header-in" label="Input file has a header line" name="header_in" truevalue="--header-in" type="boolean" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
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32 <param falsevalue="" help="--header-out" label="Print header line" name="header_out" truevalue="--header-out" type="boolean" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
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33 <param falsevalue="" help="--sort" label="Sort input" name="need_sort" truevalue="--sort" type="boolean" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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34 <param falsevalue="" help="--full" label="Print all fields from input file" name="print_full_line" truevalue="--full" type="boolean" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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35 <param falsevalue="" help="--ignore-case" label="Ignore case when grouping" name="ignore_case" truevalue="--ignore-case" type="boolean" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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36 <repeat default="1" min="1" name="operations" title="Operation to perform on each group">
1
2f3c6f2dcf39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
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37 <param name="op_name" type="select" label="Type">
0
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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38 <option value="count">count</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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39 <option value="sum">sum</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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40 <option value="min">minimum</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
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41 <option value="max">maximum</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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42 <option value="absmin">Absolute minimum</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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43 <option value="absmax">Absolute maximum</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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44 <option value="mean">Mean</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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45 <option value="pstdev">Population Standard deviantion</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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46 <option value="sstdev">Sample Standard deviantion</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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47 <option value="median">Median</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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48 <option value="q1">1st quartile</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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49 <option value="q3">3rd quartile</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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50 <option value="iqr">Inter-quartile range</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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51 <option value="mad">Median Absolute Deviation</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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52 <option value="pvar">Variance (population)</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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53 <option value="svar">Variance (sample)</option>
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54 <option value="sskew">Skewness (sample)</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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55 <option value="pskew">Skewness (population)</option>
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56 <option value="skurt">Kurtosis (sample)</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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57 <option value="pkurt">Kurtosis (population)</option>
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58 <option value="jarque">Jarque-Bera Normality test</option>
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59 <option value="dpo">DAgostino-Pearson Omnibus Normality Test</option>
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60 <option value="mode">Mode</option>
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61 <option value="antimode">Anti-Mode</option>
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62 <option value="unique">Combine all unique values</option>
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63 <option value="collapse">Combine all values</option>
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64 <option value="countunique">Count Unique values</option>
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65 </param>
1
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66 <param name="op_column" data_ref="in_file" label="On column" type="data_column" />
0
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67 </repeat>
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68 </expand>
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69 <tests>
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70 <test>
1
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71 <param name="in_file" value="group_compute_input.txt" ftype="tabular" />
0
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72 <param name="grouping" value="2" />
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73 <param name="header_in" value="true" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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74 <param name="header_out" value="true" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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75 <param name="need_sort" value="true" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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76 <param name="print_full_line" value="false" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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77 <param name="ignore_case" value="false" />
1
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78 <repeat name="operations">
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79 <param name="op_name" value="sum" />
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80 <param name="op_column" value="3" />
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81 </repeat>
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82 <output file="group_compute_output.txt" name="out_file" ftpye="tabular" />
0
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83 </test>
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84 </tests>
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85 <help>
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86 <![CDATA[
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87 @HELP_HEADER@
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88
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89 **Syntax**
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90
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91 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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92
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93 -----
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94
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95 **Example 1**
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96
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97 - 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::
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98
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99 Name Major Score
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100 Bryan Arts 68
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101 Isaiah Arts 80
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102 Gabriel Health-Medicine 100
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103 Tysza Business 92
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104 Zackery Engineering 54
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105 ...
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106 ...
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107
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108 - Grouping the input by the second column (*Major*), and performing operations **mean** and **sample standard deviation** on the third column (*Score*), gives::
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109
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110 GroupBy(Major) mean(Score) sstdev(Score)
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111 Arts 68.9474 10.4215
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112 Business 87.3636 5.18214
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113 Engineering 66.5385 19.8814
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114 Health-Medicine 90.6154 9.22441
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115 Life-Sciences 55.3333 20.606
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116 Social-Sciences 60.2667 17.2273
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117
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118 This sample file is available at http://www.gnu.org/software/datamash .
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119
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120 **Example 2**
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121
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122 - Using the UCSC RefSeq Human Gene Track, available at: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz
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123
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124 - 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::
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125
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126 GroupBy(field-13) count(field-2) collapse(field-2)
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127 A1BG 1 NM_130786
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128 A1BG-AS1 1 NR_015380
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129 A1CF 6 NM_001198818,NM_001198819,NM_001198820,NM_014576,NM_138932,NM_138933
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130 A2M 1 NM_000014
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131 A2M-AS1 1 NR_026971
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132 A2ML1 2 NM_001282424,NM_144670
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133 ...
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134
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135 - 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::
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136
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137 GroupBy(field-3) GroupBy(field-4) count(field-2)
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138 chr1 + 2456
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139 chr1 - 2431
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140 chr2 + 1599
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141 chr2 - 1419
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142 chr3 + 1287
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143 chr3 - 1249
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144 ...
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145
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146 @HELP_FOOTER@
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147 ]]>
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148 </help>
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149 </tool>