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comparison compute.xml @ 0:e91a07e82d96 draft

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First Galaxy Version
author Assaf Gordon <assafgordon@gmail.com>
date Sat, 22 Mar 2014 16:39:59 -0400
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children 16903bd2bb5b
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-1:000000000000 0:e91a07e82d96
1 <tool id="GroupCompute" name="Group and Compute" version="1.0.3">
2 <description>operations on tabular data.</description>
3
4 <requirements>
5 <requirement type="package" version="1.0.3">compute</requirement>
6 </requirements>
7
8 <command>
9 compute
10 $header_in
11 $header_out
12 $need_sort
13 $print_full_line
14 $ignore_case
15 #if str($grouping)>0
16 --group '$grouping'
17 #end if
18 -T
19 #for $oper in $operations
20 ${oper.op_name}
21 ${oper.op_column}
22 #end for
23 &lt; $in_file &gt; $out_file
24 </command>
25 <inputs>
26 <param format="tabular" name="in_file" type="data" label="Select Input Data" help=""/>
27
28 <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."/>
29
30 <param name="header_in" type="boolean" truevalue="--header-in" falsevalue=""
31 label="Input file has a header line" help="Mark this if the input file's first line is a header line" />
32
33 <param name="header_out" type="boolean" truevalue="--header-out" falsevalue=""
34 label="Print header line" help="Mark this if you want the first line to show the field names" />
35
36 <param name="need_sort" type="boolean" truevalue="--sort" falsevalue=""
37 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." />
38
39 <param name="print_full_line" type="boolean" truevalue="--full" falsevalue=""
40 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." />
41
42 <param name="ignore_case" type="boolean" truevalue="--ignore-case" falsevalue=""
43 label="Ignore case when grouping" help="If set, upper/lowercase differences will be ignored when grouping fields." />
44
45 <repeat name="operations" title="Operation to perform on each group">
46 <param name="op_name" type="select" label="Type">
47 <option value="count">count</option>
48 <option value="sum">sum</option>
49 <option value="min">minimum</option>
50 <option value="max">maximum</option>
51 <option value="absmin">Absolute minimum</option>
52 <option value="absmax">Absolute maximum</option>
53 <option value="mean">Mean</option>
54 <option value="median">Median</option>
55 <option value="mode">Mode</option>
56 <option value="antimode">Anti-Mode</option>
57 <option value="pstdev">Population Standard deviantion</option>
58 <option value="sstdev">Sample Standard deviantion</option>
59 <option value="unique">Combine all unique values</option>
60 <option value="collapse">Combine all values</option>
61 <option value="countunique">Count Unique values</option>
62 </param>
63 <param name="op_column" label="On column" type="data_column" data_ref="in_file" />
64 </repeat>
65 </inputs>
66
67 <outputs>
68 <data format="tabular" name="out_file" />
69 </outputs>
70
71 <tests>
72 <test>
73 <param name="in_file" value="group_compute_input.txt" />
74 <param name="grouping" value="2" />
75 <param name="header_in" value="true" />
76 <param name="header_out" value="true" />
77 <param name="need_sort" value="true" />
78 <param name="print_full_line" value="false" />
79 <param name="op_column" value="3" />
80 <param name="op_name" value="sum" />
81 <param name="ignore_case" value="false" />
82 <output name="out_file" file="group_compute_output.txt" />
83 </test>
84 </tests>
85 <help>
86
87 .. class:: infomark
88
89 **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.
90
91 -----
92
93 **Syntax**
94
95 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.
96
97 -----
98
99 **Example 1**
100
101 - 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::
102
103 Name Major Score
104 Bryan Arts 68
105 Isaiah Arts 80
106 Gabriel Health-Medicine 100
107 Tysza Business 92
108 Zackery Engineering 54
109 ...
110 ...
111
112 - Grouping the input by the second column (*Major*), and performing operations **mean** and **sample standard deviation** on the third column (*Score*), gives::
113
114 GroupBy(Major) mean(Score) sstdev(Score)
115 Arts 68.9474 10.4215
116 Business 87.3636 5.18214
117 Engineering 66.5385 19.8814
118 Health-Medicine 90.6154 9.22441
119 Life-Sciences 55.3333 20.606
120 Social-Sciences 60.2667 17.2273
121
122 This sample file is available at http://agordon.github.io/compute/examples.html .
123
124 **Example 2**
125
126 - Using the UCSC RefSeq Human Gene Track, available at: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz
127
128 - 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::
129
130 GroupBy(field-13) count(field-2) collapse(field-2)
131 A1BG 1 NM_130786
132 A1BG-AS1 1 NR_015380
133 A1CF 6 NM_001198818,NM_001198819,NM_001198820,NM_014576,NM_138932,NM_138933
134 A2M 1 NM_000014
135 A2M-AS1 1 NR_026971
136 A2ML1 2 NM_001282424,NM_144670
137 ...
138
139 - 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::
140
141 GroupBy(field-3) GroupBy(field-4) count(field-2)
142 chr1 + 2456
143 chr1 - 2431
144 chr2 + 1599
145 chr2 - 1419
146 chr3 + 1287
147 chr3 - 1249
148 ...
149
150 -----
151
152 **Compute** is an open-sourced program, see more details on the Compute_ Website.
153
154 **Compute** is also available as a command-line program, see http://agordon.github.io/compute/examples.html .
155
156 .. _Compute: http://agordon.github.io/compute/
157
158 </help>
159 </tool>