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comparison reorder.xml @ 31:a631c2f6d913

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Update to Miller Lab devshed revision 3c4110ffacc3
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:25:27 -0400
parents 8997f2ca8c7a
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30:4188853b940b 31:a631c2f6d913
1 <tool id="gd_reorder" name="Reorder" version="1.0.0"> 1 <tool id="gd_reorder" name="Reorder individuals" version="1.0.0">
2 <description>individuals</description> 2 <description>: exchange rows in the above picture</description>
3 3
4 <command interpreter="python"> 4 <command interpreter="python">
5 reorder.py '$input' '$output' '$order' 5 reorder.py '$input' '$output' '$order'
6 </command> 6 </command>
7 7
13 <outputs> 13 <outputs>
14 <data name="output" format="gd_indivs" metadata_source="input"/> 14 <data name="output" format="gd_indivs" metadata_source="input"/>
15 </outputs> 15 </outputs>
16 16
17 <help> 17 <help>
18 **Dataset formats**
19
20 The input and output datasets are in gd_indivs_ format.
21
22 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
23
24 -----
25
26 **What it does**
27
28 The user picks a gd_indivs dataset from their history and specifies
29 a new ordering. This tool creates a new gd_indivs dataset with the
30 individuals reordered as specified by the user.
31
32 The new ordering is a list of comma separated ranges (e.g **5,6-12,20**).
33 Ranges can be either a single number (e.g. **3**) or two dash separated
34 numbers (e.g. **3-5**). The numbers represent the line number of
35 gd_indivs dataset. Line numbers that are not listed will appear on the
36 output after the specified line numbers in their same relative ordering.
37
38 -----
39
40 **Example**
41
42 Input dataset (six rows)::
43
44 18 McClintock
45 22 Peltonen-Palotie
46 26 Sager
47 30 Franklin
48 34 Auerbach
49 38 Stevens
50
51 new ordering "**1,3-4**" will return::
52
53 18 McClintock
54 26 Sager
55 30 Franklin
56 22 Peltonen-Palotie
57 34 Auerbach
58 38 Stevens
59
60 new ordering "**3,5,1,6**" will return::
61
62 26 Sager
63 34 Auerbach
64 18 McClintock
65 38 Stevens
66 22 Peltonen-Palotie
67 30 Franklin
68
69 new ordering "**3-1,6,4-5**" will return::
70
71 26 Sager
72 22 Peltonen-Palotie
73 18 McClintock
74 38 Stevens
75 30 Franklin
76 34 Auerbach
18 </help> 77 </help>
19 </tool> 78 </tool>