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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit c196ca939107154dbcfa84ed34fb01655f4fc59f-dirty
author iuc
date Wed, 14 Oct 2015 16:19:37 -0400
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1 <?xml version="1.0"?>
2 <tool id="DatamashOps" name="Datamash" version="1.0.6">
3 <description>(operations on tabular data)</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <command>
10 <![CDATA[
11 datamash
12 $header_in
13 $header_out
14 $need_sort
15 $print_full_line
16 $ignore_case
17 #if str($grouping).strip()
18 --group '$grouping'
19 #end if
20 #for $oper in $operations
21 ${oper.op_name}
22 ${oper.op_column}
23 #end for
24 < $in_file > $out_file
25 ]]>
26 </command>
27 <expand macro="inputs_outputs">
28 <param help="Example: to group by the first and fourth fields, use 1,4." label="Group by fields" name="grouping" type="text">
29 <validator message="Invalid value in field. Allowed values are 0-9, space, comma." type="regex">^[0-9, ]*$</validator>
30 </param>
31 <param falsevalue="" help="--header-in" label="Input file has a header line" name="header_in" truevalue="--header-in" type="boolean" />
32 <param falsevalue="" help="--header-out" label="Print header line" name="header_out" truevalue="--header-out" type="boolean" />
33 <param falsevalue="" help="--sort" label="Sort input" name="need_sort" truevalue="--sort" type="boolean" />
34 <param falsevalue="" help="--full" label="Print all fields from input file" name="print_full_line" truevalue="--full" type="boolean" />
35 <param falsevalue="" help="--ignore-case" label="Ignore case when grouping" name="ignore_case" truevalue="--ignore-case" type="boolean" />
36 <repeat default="1" min="1" name="operations" title="Operation to perform on each group">
37 <param label="Type" name="op_name" type="select">
38 <option value="count">count</option>
39 <option value="sum">sum</option>
40 <option value="min">minimum</option>
41 <option value="max">maximum</option>
42 <option value="absmin">Absolute minimum</option>
43 <option value="absmax">Absolute maximum</option>
44 <option value="mean">Mean</option>
45 <option value="pstdev">Population Standard deviantion</option>
46 <option value="sstdev">Sample Standard deviantion</option>
47 <option value="median">Median</option>
48 <option value="q1">1st quartile</option>
49 <option value="q3">3rd quartile</option>
50 <option value="iqr">Inter-quartile range</option>
51 <option value="mad">Median Absolute Deviation</option>
52 <option value="pvar">Variance (population)</option>
53 <option value="svar">Variance (sample)</option>
54 <option value="sskew">Skewness (sample)</option>
55 <option value="pskew">Skewness (population)</option>
56 <option value="skurt">Kurtosis (sample)</option>
57 <option value="pkurt">Kurtosis (population)</option>
58 <option value="jarque">Jarque-Bera Normality test</option>
59 <option value="dpo">DAgostino-Pearson Omnibus Normality Test</option>
60 <option value="mode">Mode</option>
61 <option value="antimode">Anti-Mode</option>
62 <option value="unique">Combine all unique values</option>
63 <option value="collapse">Combine all values</option>
64 <option value="countunique">Count Unique values</option>
65 </param>
66 <param data_ref="in_file" label="On column" name="op_column" type="data_column" />
67 </repeat>
68 </expand>
69 <tests>
70 <test>
71 <param name="in_file" value="group_compute_input.txt" />
72 <param name="grouping" value="2" />
73 <param name="header_in" value="true" />
74 <param name="header_out" value="true" />
75 <param name="need_sort" value="true" />
76 <param name="print_full_line" value="false" />
77 <param name="op_column" value="3" />
78 <param name="op_name" value="sum" />
79 <param name="ignore_case" value="false" />
80 <output file="group_compute_output.txt" name="out_file" />
81 </test>
82 </tests>
83 <help>
84 <![CDATA[
85 @HELP_HEADER@
86
87 **Syntax**
88
89 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.
90
91 -----
92
93 **Example 1**
94
95 - 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::
96
97 Name Major Score
98 Bryan Arts 68
99 Isaiah Arts 80
100 Gabriel Health-Medicine 100
101 Tysza Business 92
102 Zackery Engineering 54
103 ...
104 ...
105
106 - Grouping the input by the second column (*Major*), and performing operations **mean** and **sample standard deviation** on the third column (*Score*), gives::
107
108 GroupBy(Major) mean(Score) sstdev(Score)
109 Arts 68.9474 10.4215
110 Business 87.3636 5.18214
111 Engineering 66.5385 19.8814
112 Health-Medicine 90.6154 9.22441
113 Life-Sciences 55.3333 20.606
114 Social-Sciences 60.2667 17.2273
115
116 This sample file is available at http://www.gnu.org/software/datamash .
117
118 **Example 2**
119
120 - Using the UCSC RefSeq Human Gene Track, available at: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz
121
122 - 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::
123
124 GroupBy(field-13) count(field-2) collapse(field-2)
125 A1BG 1 NM_130786
126 A1BG-AS1 1 NR_015380
127 A1CF 6 NM_001198818,NM_001198819,NM_001198820,NM_014576,NM_138932,NM_138933
128 A2M 1 NM_000014
129 A2M-AS1 1 NR_026971
130 A2ML1 2 NM_001282424,NM_144670
131 ...
132
133 - 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::
134
135 GroupBy(field-3) GroupBy(field-4) count(field-2)
136 chr1 + 2456
137 chr1 - 2431
138 chr2 + 1599
139 chr2 - 1419
140 chr3 + 1287
141 chr3 - 1249
142 ...
143
144 @HELP_FOOTER@
145 ]]>
146 </help>
147 </tool>