Mercurial > repos > iuc > datamash_ops

annotate datamash-ops.xml @ 2:562f3c677828 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author iuc
date Fri, 07 Sep 2018 10:58:27 -0400
parents 2f3c6f2dcf39
children 419027d822d6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
2
562f3c677828 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 1
diff changeset
2 <tool id="datamash_ops" name="Datamash" version="@WRAPPER_VERSION@">
0
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
3 <description>(operations on tabular data)</description>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
4 <macros>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
5 <import>macros.xml</import>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
6 </macros>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
7 <expand macro="requirements" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
8 <expand macro="stdio" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
9 <command>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
10 <![CDATA[
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
11 datamash
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
12 $header_in
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
13 $header_out
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
14 $need_sort
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
15 $print_full_line
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
16 $ignore_case
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
17 #if str($grouping).strip()
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
18 --group '$grouping'
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
19 #end if
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
20 #for $oper in $operations
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
21 ${oper.op_name}
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
22 ${oper.op_column}
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
23 #end for
2
562f3c677828 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 1
diff changeset
24 < $in_file > '$out_file'
0
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
25 ]]>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
26 </command>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
27 <expand macro="inputs_outputs">
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
28 <param help="Example: to group by the first and fourth fields, use 1,4." label="Group by fields" name="grouping" type="text">
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
29 <validator message="Invalid value in field. Allowed values are 0-9, space, comma." type="regex">^[0-9, ]*$</validator>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
30 </param>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
31 <param falsevalue="" help="--header-in" label="Input file has a header line" name="header_in" truevalue="--header-in" type="boolean" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
32 <param falsevalue="" help="--header-out" label="Print header line" name="header_out" truevalue="--header-out" type="boolean" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
33 <param falsevalue="" help="--sort" label="Sort input" name="need_sort" truevalue="--sort" type="boolean" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
34 <param falsevalue="" help="--full" label="Print all fields from input file" name="print_full_line" truevalue="--full" type="boolean" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
35 <param falsevalue="" help="--ignore-case" label="Ignore case when grouping" name="ignore_case" truevalue="--ignore-case" type="boolean" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
36 <repeat default="1" min="1" name="operations" title="Operation to perform on each group">
1
2f3c6f2dcf39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
parents: 0
diff changeset
37 <param name="op_name" type="select" label="Type">
0
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
38 <option value="count">count</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
39 <option value="sum">sum</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
40 <option value="min">minimum</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
41 <option value="max">maximum</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
42 <option value="absmin">Absolute minimum</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
43 <option value="absmax">Absolute maximum</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
44 <option value="mean">Mean</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
45 <option value="pstdev">Population Standard deviantion</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
46 <option value="sstdev">Sample Standard deviantion</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
47 <option value="median">Median</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
48 <option value="q1">1st quartile</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
49 <option value="q3">3rd quartile</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
50 <option value="iqr">Inter-quartile range</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
51 <option value="mad">Median Absolute Deviation</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
52 <option value="pvar">Variance (population)</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
53 <option value="svar">Variance (sample)</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
54 <option value="sskew">Skewness (sample)</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
55 <option value="pskew">Skewness (population)</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
56 <option value="skurt">Kurtosis (sample)</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
57 <option value="pkurt">Kurtosis (population)</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
58 <option value="jarque">Jarque-Bera Normality test</option>
2
562f3c677828 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 1
diff changeset
59 <option value="dpo">D Agostino-Pearson Omnibus Normality Test</option>
0
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
60 <option value="mode">Mode</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
61 <option value="antimode">Anti-Mode</option>
2
562f3c677828 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 1
diff changeset
62 <option value="rand">One random value from the group</option>
0
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
63 <option value="unique">Combine all unique values</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
64 <option value="collapse">Combine all values</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
65 <option value="countunique">Count Unique values</option>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
66 </param>
1
2f3c6f2dcf39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
parents: 0
diff changeset
67 <param name="op_column" data_ref="in_file" label="On column" type="data_column" />
0
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
68 </repeat>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
69 </expand>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
70 <tests>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
71 <test>
1
2f3c6f2dcf39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
parents: 0
diff changeset
72 <param name="in_file" value="group_compute_input.txt" ftype="tabular" />
0
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
73 <param name="grouping" value="2" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
74 <param name="header_in" value="true" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
75 <param name="header_out" value="true" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
76 <param name="need_sort" value="true" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
77 <param name="print_full_line" value="false" />
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
78 <param name="ignore_case" value="false" />
1
2f3c6f2dcf39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
parents: 0
diff changeset
79 <repeat name="operations">
2f3c6f2dcf39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
parents: 0
diff changeset
80 <param name="op_name" value="sum" />
2f3c6f2dcf39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
parents: 0
diff changeset
81 <param name="op_column" value="3" />
2f3c6f2dcf39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
parents: 0
diff changeset
82 </repeat>
2
562f3c677828 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 1
diff changeset
83 <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
iuc
parents:
diff changeset
84 </test>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
85 </tests>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
86 <help>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
87 <![CDATA[
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
88 @HELP_HEADER@
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
89
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
90 **Syntax**
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
91
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
92 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.
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
93
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
94 -----
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
95
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
96 **Example 1**
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
97
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
98 - 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
iuc
parents:
diff changeset
99
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
100 Name Major Score
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
101 Bryan Arts 68
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
102 Isaiah Arts 80
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
103 Gabriel Health-Medicine 100
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
104 Tysza Business 92
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
105 Zackery Engineering 54
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
106 ...
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
107 ...
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
108
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
109 - Grouping the input by the second column (*Major*), and performing operations **mean** and **sample standard deviation** on the third column (*Score*), gives::
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
110
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
111 GroupBy(Major) mean(Score) sstdev(Score)
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
112 Arts 68.9474 10.4215
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
113 Business 87.3636 5.18214
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
114 Engineering 66.5385 19.8814
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
115 Health-Medicine 90.6154 9.22441
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
116 Life-Sciences 55.3333 20.606
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
117 Social-Sciences 60.2667 17.2273
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
118
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
119 This sample file is available at http://www.gnu.org/software/datamash .
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
120
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
121 **Example 2**
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
122
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
123 - Using the UCSC RefSeq Human Gene Track, available at: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
124
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
125 - 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
iuc
parents:
diff changeset
126
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
127 GroupBy(field-13) count(field-2) collapse(field-2)
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
128 A1BG 1 NM_130786
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
129 A1BG-AS1 1 NR_015380
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
130 A1CF 6 NM_001198818,NM_001198819,NM_001198820,NM_014576,NM_138932,NM_138933
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
131 A2M 1 NM_000014
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
132 A2M-AS1 1 NR_026971
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
133 A2ML1 2 NM_001282424,NM_144670
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
134 ...
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
135
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
136 - 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::
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
137
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
138 GroupBy(field-3) GroupBy(field-4) count(field-2)
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
139 chr1 + 2456
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
140 chr1 - 2431
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
141 chr2 + 1599
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
142 chr2 - 1419
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
143 chr3 + 1287
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
144 chr3 - 1249
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
145 ...
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
146
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
147 @HELP_FOOTER@
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
148 ]]>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
149 </help>
c4611129661b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff changeset
150 </tool>