Mercurial > repos > iuc > datamash_ops

annotate datamash-ops.xml @ 4:746e8e4bf929 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 384736acb5d2ae31d796c53031fad0e5da5424e3
author iuc
date Fri, 01 Jul 2022 16:18:07 +0000
parents 419027d822d6
children 4c07ddedc198
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419027d822d6 "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" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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10 datamash
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11 $header_in
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12 $header_out
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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13 $need_sort
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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14 $print_full_line
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15 $ignore_case
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16 $narm
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17 @FIELD_SEPARATOR@
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18 #if str($grouping) != ''
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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19 --group '$grouping'
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20 #end if
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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21 #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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22 ${oper.op_name}
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23 ${oper.op_column}
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24 #end for
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25 < $in_file > '$out_file'
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26 ]]>
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27 </command>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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28 <expand macro="inputs_outputs">
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29 <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">
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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30 <sanitizer invalid_char="">
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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31 <valid initial="string.digits">
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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32 <add value="," />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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33 </valid>
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34 <mapping initial="none">
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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35 <add source=" " target=""/>
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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36 </mapping>
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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37 </sanitizer>
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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38 <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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39 </param>
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40 <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."/>
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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41 <param argument="--header-in" type="boolean" truevalue="--header-in" falsevalue="" label="Input file has a header line" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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42 <param argument="--header-out" type="boolean" truevalue="--header-out" falsevalue="" label="Print header line" />
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43 <param argument="--full" name="print_full_line" type="boolean" truevalue="--full" falsevalue="" label="Print all fields from input file" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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44 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" label="Ignore case when grouping" />
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45 <param argument="--narm" type="boolean" truevalue="--narm" falsevalue="" label="Skip NA or NaN values" />
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46 <repeat name="operations" default="1" min="1" title="Operation to perform on each group">
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47 <param name="op_name" type="select" label="Type">
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48 <option value="count">count</option>
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49 <option value="sum">sum</option>
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50 <option value="min">minimum</option>
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51 <option value="max">maximum</option>
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52 <option value="absmin">Absolute minimum</option>
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53 <option value="absmax">Absolute maximum</option>
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54 <option value="mean">Mean</option>
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55 <option value="pstdev">Population Standard deviantion</option>
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56 <option value="sstdev">Sample Standard deviantion</option>
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57 <option value="median">Median</option>
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58 <option value="q1">1st quartile</option>
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59 <option value="q3">3rd quartile</option>
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60 <option value="iqr">Inter-quartile range</option>
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61 <option value="mad">Median Absolute Deviation</option>
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62 <option value="pvar">Variance (population)</option>
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63 <option value="svar">Variance (sample)</option>
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64 <option value="sskew">Skewness (sample)</option>
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65 <option value="pskew">Skewness (population)</option>
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66 <option value="skurt">Kurtosis (sample)</option>
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67 <option value="pkurt">Kurtosis (population)</option>
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68 <option value="jarque">Jarque-Bera Normality test</option>
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69 <option value="dpo">D Agostino-Pearson Omnibus Normality Test</option>
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70 <option value="mode">Mode</option>
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71 <option value="antimode">Anti-Mode</option>
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72 <option value="rand">One random value from the group</option>
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73 <option value="unique">Combine all unique values</option>
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74 <option value="collapse">Combine all values</option>
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75 <option value="countunique">Count Unique values</option>
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76 </param>
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77 <param name="op_column" data_ref="in_file" label="On column" type="data_column" />
0
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78 </repeat>
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79 </expand>
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80 <tests>
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81 <test>
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82 <param name="in_file" value="group_compute_input.txt" ftype="tabular" />
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83 <param name="grouping" value="2" />
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84 <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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85 <param name="header_out" value="true" />
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86 <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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87 <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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88 <param name="ignore_case" value="false" />
1
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89 <repeat name="operations">
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90 <param name="op_name" value="sum" />
2f3c6f2dcf39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
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91 <param name="op_column" value="3" />
2f3c6f2dcf39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
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92 </repeat>
2
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93 <output file="group_compute_output.txt" name="out_file" ftype="tabular" />
0
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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94 </test>
3
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95 <test>
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96 <param name="in_file" value="group_compute_input.txt" ftype="tsv" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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97 <param name="grouping" value="2" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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98 <param name="header_in" value="true" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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99 <param name="header_out" value="true" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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100 <param name="need_sort" value="true" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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101 <param name="print_full_line" value="false" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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102 <param name="ignore_case" value="false" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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103 <repeat name="operations">
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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104 <param name="op_name" value="sum" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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105 <param name="op_column" value="3" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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106 </repeat>
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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107 <output file="group_compute_output.txt" name="out_file" ftype="tsv" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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108 </test>
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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109 <test>
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110 <param name="in_file" value="group_compute_input.csv" ftype="csv" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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111 <param name="grouping" value="2" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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112 <param name="header_in" value="true" />
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113 <param name="header_out" value="true" />
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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114 <param name="need_sort" value="true" />
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115 <param name="print_full_line" value="false" />
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116 <param name="ignore_case" value="false" />
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117 <repeat name="operations">
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118 <param name="op_name" value="sum" />
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119 <param name="op_column" value="3" />
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120 </repeat>
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121 <output name="out_file" ftype="csv">
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122 <assert_contents>
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123 <has_n_lines n="7"/>
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124 <has_line line="Arts,1310"/>
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125 </assert_contents>
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126 </output>
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127 </test>
4
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128 <test><!-- test with a file containing NA and NaN values and the -narm parameter " -->
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129 <param name="in_file" value="na_values_input.tsv" ftype="tabular" />
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130 <param name="grouping" value="2" />
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131 <param name="header_in" value="true" />
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132 <param name="print_full_line" value="false" />
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133 <param name="need_sort" value="true" />
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134 <param name="narm" value="true" />
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135 <repeat name="operations">
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136 <param name="op_name" value="mean" />
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137 <param name="op_column" value="3" />
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138 </repeat>
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139 <output name="out_file" ftype="tabular">
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140 <assert_contents>
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141 <has_n_lines n="2"/>
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142 <has_line_matching expression="DE\t173.5"/>
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143 <has_line_matching expression="NL\t177.5"/>
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144 </assert_contents>
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145 </output>
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146 </test>
0
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147 </tests>
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148 <help>
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149 <![CDATA[
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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150 @HELP_HEADER@
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151
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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152 **Syntax**
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153
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154 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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155
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156 -----
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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157
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158 **Example 1**
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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159
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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160 - 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::
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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161
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162 Name Major Score
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163 Bryan Arts 68
3
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164 Gabriel Health-Medicine 100
0
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165 Isaiah Arts 80
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166 Tysza Business 92
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167 Zackery Engineering 54
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168 ...
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169 ...
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170
3
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171 - 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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172
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173 GroupBy(Major) mean(Score) sstdev(Score)
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174 Arts 68.9474 10.4215
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175 Business 87.3636 5.18214
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176 Engineering 66.5385 19.8814
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177 Health-Medicine 90.6154 9.22441
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178 Life-Sciences 55.3333 20.606
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179 Social-Sciences 60.2667 17.2273
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180
3
419027d822d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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181 Note that input needs sorting here, since the column used for grouping (*Major*) is not sorted.
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182
0
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183 This sample file is available at http://www.gnu.org/software/datamash .
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184
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185 **Example 2**
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186
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187 - Using the UCSC RefSeq Human Gene Track, available at: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz
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188
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189 - 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::
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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190
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191 GroupBy(field-13) count(field-2) collapse(field-2)
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192 A1BG 1 NM_130786
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193 A1BG-AS1 1 NR_015380
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194 A1CF 6 NM_001198818,NM_001198819,NM_001198820,NM_014576,NM_138932,NM_138933
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195 A2M 1 NM_000014
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196 A2M-AS1 1 NR_026971
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197 A2ML1 2 NM_001282424,NM_144670
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198 ...
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199
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200 - 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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201
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202 GroupBy(field-3) GroupBy(field-4) count(field-2)
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203 chr1 + 2456
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204 chr1 - 2431
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205 chr2 + 1599
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206 chr2 - 1419
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207 chr3 + 1287
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208 chr3 - 1249
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209 ...
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210
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211 @HELP_FOOTER@
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212 ]]>
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213 </help>
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214 </tool>