Mercurial > repos > iuc > datamash_ops

annotate datamash-ops.xml @ 9:4b7dd5ff6497 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 16:15:57 +0000
parents f11dedb74b83
children 67d9cf45e802
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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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16 $narm
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17 @FIELD_SEPARATOR@
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18 #if str($grouping) != ''
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19 --group '$grouping'
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20 #end if
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21 #for $oper in $operations
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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>
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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">
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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30 <sanitizer invalid_char="">
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31 <valid initial="string.digits">
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32 <add value="," />
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33 </valid>
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34 <mapping initial="none">
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35 <add source=" " target=""/>
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36 </mapping>
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37 </sanitizer>
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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."/>
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41 <param argument="--header-in" type="boolean" truevalue="--header-in" falsevalue="" label="Input file has a header line" />
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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" />
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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" />
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85 <param name="header_out" value="true" />
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
iuc
parents:
diff changeset
86 <param name="need_sort" value="true" />
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
iuc
parents:
diff changeset
87 <param name="print_full_line" value="false" />
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
iuc
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88 <param name="ignore_case" value="false" />
4
7ae1fa51bacf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
parents: 0
diff changeset
89 <repeat name="operations">
7ae1fa51bacf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
parents: 0
diff changeset
90 <param name="op_name" value="sum" />
7ae1fa51bacf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
parents: 0
diff changeset
91 <param name="op_column" value="3" />
7ae1fa51bacf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
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92 </repeat>
5
90ff417a72fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 7409e73927c65e293ad19d54bb2572b4a289929d
iuc
parents: 4
diff changeset
93 <output file="group_compute_output.txt" name="out_file" ftype="tabular" />
0
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
iuc
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94 </test>
8
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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95 <test>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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96 <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"
iuc
parents: 7
diff changeset
97 <param name="grouping" value="2" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents: 7
diff changeset
98 <param name="header_in" value="true" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents: 7
diff changeset
99 <param name="header_out" value="true" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
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100 <param name="need_sort" value="true" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
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101 <param name="print_full_line" value="false" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents: 7
diff changeset
102 <param name="ignore_case" value="false" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents: 7
diff changeset
103 <repeat name="operations">
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
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diff changeset
104 <param name="op_name" value="sum" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
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diff changeset
105 <param name="op_column" value="3" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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106 </repeat>
f11dedb74b83 "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" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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108 </test>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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109 <test>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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110 <param name="in_file" value="group_compute_input.csv" ftype="csv" />
f11dedb74b83 "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" />
f11dedb74b83 "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" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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113 <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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114 <param name="need_sort" value="true" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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115 <param name="print_full_line" value="false" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
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116 <param name="ignore_case" value="false" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
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117 <repeat name="operations">
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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118 <param name="op_name" value="sum" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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119 <param name="op_column" value="3" />
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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120 </repeat>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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121 <output name="out_file" ftype="csv">
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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122 <assert_contents>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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123 <has_n_lines n="7"/>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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124 <has_line line="Arts,1310"/>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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125 </assert_contents>
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126 </output>
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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127 </test>
9
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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" />
4b7dd5ff6497 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 384736acb5d2ae31d796c53031fad0e5da5424e3
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130 <param name="grouping" value="2" />
4b7dd5ff6497 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 384736acb5d2ae31d796c53031fad0e5da5424e3
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131 <param name="header_in" value="true" />
4b7dd5ff6497 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 384736acb5d2ae31d796c53031fad0e5da5424e3
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132 <param name="print_full_line" value="false" />
4b7dd5ff6497 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 384736acb5d2ae31d796c53031fad0e5da5424e3
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133 <param name="need_sort" value="true" />
4b7dd5ff6497 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 384736acb5d2ae31d796c53031fad0e5da5424e3
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134 <param name="narm" value="true" />
4b7dd5ff6497 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 384736acb5d2ae31d796c53031fad0e5da5424e3
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135 <repeat name="operations">
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136 <param name="op_name" value="mean" />
4b7dd5ff6497 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 384736acb5d2ae31d796c53031fad0e5da5424e3
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137 <param name="op_column" value="3" />
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138 </repeat>
4b7dd5ff6497 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 384736acb5d2ae31d796c53031fad0e5da5424e3
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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"/>
4b7dd5ff6497 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 384736acb5d2ae31d796c53031fad0e5da5424e3
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142 <has_line_matching expression="DE\t173.5"/>
4b7dd5ff6497 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 384736acb5d2ae31d796c53031fad0e5da5424e3
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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>
4b7dd5ff6497 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 384736acb5d2ae31d796c53031fad0e5da5424e3
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146 </test>
0
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147 </tests>
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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148 <help>
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149 <![CDATA[
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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150 @HELP_HEADER@
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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151
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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152 **Syntax**
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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153
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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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.
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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155
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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156 -----
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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157
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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158 **Example 1**
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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159
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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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::
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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161
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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162 Name Major Score
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163 Bryan Arts 68
8
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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164 Gabriel Health-Medicine 100
0
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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165 Isaiah Arts 80
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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166 Tysza Business 92
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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167 Zackery Engineering 54
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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168 ...
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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169 ...
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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170
8
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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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
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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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
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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175 Business 87.3636 5.18214
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176 Engineering 66.5385 19.8814
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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177 Health-Medicine 90.6154 9.22441
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178 Life-Sciences 55.3333 20.606
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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179 Social-Sciences 60.2667 17.2273
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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180
8
f11dedb74b83 "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.
f11dedb74b83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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182
0
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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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::
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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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
2d03f8df7806 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
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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>