annotate datamash-ops.xml @ 9:fecc95defba2

tool-deps.xml: update correct revision/name
author Assaf Gordon <agordon@wi.mit.edu>
date Sat, 22 Nov 2014 20:43:20 -0500
parents 22080cbb0e2a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
34752e3c7bc7 rename tool id to 'DatamashOps'
Assaf Gordon <agordon@wi.mit.edu>
parents: 3
diff changeset
1 <tool id="DatamashOps" name="Datamash" version="1.0.6">
2
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
2 <description>(operations on tabular data)</description>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
3
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
4 <requirements>
3
c553b0d578d9 Update 'datamash' to version 1.0.6
Assaf Gordon <agordon@wi.mit.edu>
parents: 2
diff changeset
5 <requirement type="package" version="1.0.6">datamash</requirement>
2
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
6 </requirements>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
7
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
8 <command>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
9 datamash
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
10 $header_in
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
11 $header_out
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
12 $need_sort
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
13 $print_full_line
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
14 $ignore_case
6
22080cbb0e2a datamash: improve XML tool
Assaf Gordon <agordon@wi.mit.edu>
parents: 5
diff changeset
15 #if str($grouping).strip()
2
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
16 --group '$grouping'
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
17 #end if
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
18 #for $oper in $operations
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
19 ${oper.op_name}
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
20 ${oper.op_column}
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
21 #end for
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
22 &lt; $in_file &gt; $out_file
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
23 </command>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
24 <inputs>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
25 <param format="tabular" name="in_file" type="data" label="Select Input Data" help=""/>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
26
6
22080cbb0e2a datamash: improve XML tool
Assaf Gordon <agordon@wi.mit.edu>
parents: 5
diff changeset
27 <param name="grouping" label="Group by fields" type="text" help="Example: 1,4 - To group by the first and fourth fields. Leave empty to perform operation on entire file as one group.">
22080cbb0e2a datamash: improve XML tool
Assaf Gordon <agordon@wi.mit.edu>
parents: 5
diff changeset
28 <validator type="regex" message="invalid fields value">^[0-9, ]*$</validator>
22080cbb0e2a datamash: improve XML tool
Assaf Gordon <agordon@wi.mit.edu>
parents: 5
diff changeset
29 </param>
2
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
30
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
31 <param name="header_in" type="boolean" truevalue="--header-in" falsevalue=""
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
32 label="Input file has a header line" help="Mark this if the input file's first line is a header line" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
33
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
34 <param name="header_out" type="boolean" truevalue="--header-out" falsevalue=""
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
35 label="Print header line" help="Mark this if you want the first line to show the field names" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
36
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
37 <param name="need_sort" type="boolean" truevalue="--sort" falsevalue=""
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
38 label="Sort input" help="Mark if the input file is not sorted. If the input file is already sorted, unmark this option to reduce computing time." />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
39
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
40 <param name="print_full_line" type="boolean" truevalue="--full" falsevalue=""
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
41 label="Print all fields from input file" help="If set, all input fields will be printed. If unset, only fields used for grouping will be printed." />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
42
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
43 <param name="ignore_case" type="boolean" truevalue="--ignore-case" falsevalue=""
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
44 label="Ignore case when grouping" help="If set, upper/lowercase differences will be ignored when grouping fields." />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
45
6
22080cbb0e2a datamash: improve XML tool
Assaf Gordon <agordon@wi.mit.edu>
parents: 5
diff changeset
46 <repeat name="operations" title="Operation to perform on each group" min="1" default="1">
2
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
47 <param name="op_name" type="select" label="Type">
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
48 <option value="count">count</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
49 <option value="sum">sum</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
50 <option value="min">minimum</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
51 <option value="max">maximum</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
52 <option value="absmin">Absolute minimum</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
53 <option value="absmax">Absolute maximum</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
54 <option value="mean">Mean</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
55 <option value="pstdev">Population Standard deviantion</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
56 <option value="sstdev">Sample Standard deviantion</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
57 <option value="median">Median</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
58 <option value="q1">1st quartile</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
59 <option value="q3">3rd quartile</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
60 <option value="iqr">Inter-quartile range</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
61 <option value="mad">Median Absolute Deviation</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
62 <option value="pvar">Variance (population)</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
63 <option value="svar">Variance (sample)</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
64 <option value="sskew">Skewness (sample)</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
65 <option value="pskew">Skewness (population)</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
66 <option value="skurt">Kurtosis (sample)</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
67 <option value="pkurt">Kurtosis (population)</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
68 <option value="jarque">Jarque-Bera Normality test</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
69 <option value="dpo">DAgostino-Pearson Omnibus Normality Test</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
70 <option value="mode">Mode</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
71 <option value="antimode">Anti-Mode</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
72 <option value="unique">Combine all unique values</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
73 <option value="collapse">Combine all values</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
74 <option value="countunique">Count Unique values</option>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
75 </param>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
76 <param name="op_column" label="On column" type="data_column" data_ref="in_file" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
77 </repeat>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
78 </inputs>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
79
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
80 <outputs>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
81 <data format="tabular" name="out_file" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
82 </outputs>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
83
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
84 <tests>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
85 <test>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
86 <param name="in_file" value="group_compute_input.txt" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
87 <param name="grouping" value="2" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
88 <param name="header_in" value="true" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
89 <param name="header_out" value="true" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
90 <param name="need_sort" value="true" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
91 <param name="print_full_line" value="false" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
92 <param name="op_column" value="3" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
93 <param name="op_name" value="sum" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
94 <param name="ignore_case" value="false" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
95 <output name="out_file" file="group_compute_output.txt" />
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
96 </test>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
97 </tests>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
98 <help>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
99
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
100 .. class:: infomark
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
101
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
102 **TIP:** Input data must be TAB delimited. If the desired dataset does not appear in the input list, use *Text Manipulation-&gt;Convert* to convert it to **Tabular** type.
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
103
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
104 -----
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
105
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
106 **Syntax**
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
107
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
108 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.
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
109
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
110 -----
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
111
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
112 **Example 1**
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
113
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
114 - 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::
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
115
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
116 Name Major Score
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
117 Bryan Arts 68
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
118 Isaiah Arts 80
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
119 Gabriel Health-Medicine 100
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
120 Tysza Business 92
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
121 Zackery Engineering 54
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
122 ...
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
123 ...
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
124
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
125 - Grouping the input by the second column (*Major*), and performing operations **mean** and **sample standard deviation** on the third column (*Score*), gives::
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
126
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
127 GroupBy(Major) mean(Score) sstdev(Score)
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
128 Arts 68.9474 10.4215
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
129 Business 87.3636 5.18214
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
130 Engineering 66.5385 19.8814
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
131 Health-Medicine 90.6154 9.22441
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
132 Life-Sciences 55.3333 20.606
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
133 Social-Sciences 60.2667 17.2273
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
134
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
135 This sample file is available at http://www.gnu.org/software/datamash .
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
136
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
137 **Example 2**
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
138
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
139 - Using the UCSC RefSeq Human Gene Track, available at: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
140
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
141 - 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::
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
142
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
143 GroupBy(field-13) count(field-2) collapse(field-2)
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
144 A1BG 1 NM_130786
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
145 A1BG-AS1 1 NR_015380
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
146 A1CF 6 NM_001198818,NM_001198819,NM_001198820,NM_014576,NM_138932,NM_138933
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
147 A2M 1 NM_000014
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
148 A2M-AS1 1 NR_026971
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
149 A2ML1 2 NM_001282424,NM_144670
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
150 ...
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
151
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
152 - 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::
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
153
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
154 GroupBy(field-3) GroupBy(field-4) count(field-2)
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
155 chr1 + 2456
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
156 chr1 - 2431
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
157 chr2 + 1599
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
158 chr2 - 1419
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
159 chr3 + 1287
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
160 chr3 - 1249
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
161 ...
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
162
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
163 -----
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
164
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
165 **GNU Datamash** is a Free and Open Source Software, see more details on the Datamash_ Website.
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
166
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
167 **GNU Datamash** is also available as a command-line program, see http://www.gnu.org/software/datamash/download/ .
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
168
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
169 For more details about supported statistical operations, see Datamash_ website.
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
170
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
171 .. _Datamash: http://www.gnu.org/software/datamash/
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
172
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
173 </help>
3d4113adbb9c GNU Datamash, version 1.0.5, galaxy tool v1.
Assaf Gordon <assafgordon@gmail.com>
parents:
diff changeset
174 </tool>