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annotate reorder.xml @ 36:51cd0307fb70

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Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
parents a631c2f6d913
children
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1 <tool id="gd_reorder" name="Reorder individuals" version="1.0.0">
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2 <description>: exchange rows in the above picture</description>
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3
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4 <command interpreter="python">
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5 reorder.py '$input' '$output' '$order'
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6 </command>
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7
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8 <inputs>
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9 <param name="input" type="data" format="gd_indivs" label="Individuals dataset" />
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10 <param name="order" size="40" type="text" value="" label="New order"/>
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11 </inputs>
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12
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13 <outputs>
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14 <data name="output" format="gd_indivs" metadata_source="input"/>
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15 </outputs>
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16
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17 <help>
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18 **Dataset formats**
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19
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20 The input and output datasets are in gd_indivs_ format.
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22 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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23
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24 -----
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25
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26 **What it does**
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28 The user picks a gd_indivs dataset from their history and specifies
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29 a new ordering. This tool creates a new gd_indivs dataset with the
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30 individuals reordered as specified by the user.
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31
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32 The new ordering is a list of comma separated ranges (e.g **5,6-12,20**).
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33 Ranges can be either a single number (e.g. **3**) or two dash separated
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34 numbers (e.g. **3-5**). The numbers represent the line number of
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35 gd_indivs dataset. Line numbers that are not listed will appear on the
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36 output after the specified line numbers in their same relative ordering.
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37
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38 -----
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39
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40 **Example**
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41
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42 Input dataset (six rows)::
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43
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44 18 McClintock
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45 22 Peltonen-Palotie
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46 26 Sager
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47 30 Franklin
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48 34 Auerbach
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49 38 Stevens
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51 new ordering "**1,3-4**" will return::
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53 18 McClintock
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54 26 Sager
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55 30 Franklin
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56 22 Peltonen-Palotie
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57 34 Auerbach
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58 38 Stevens
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60 new ordering "**3,5,1,6**" will return::
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62 26 Sager
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63 34 Auerbach
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64 18 McClintock
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65 38 Stevens
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66 22 Peltonen-Palotie
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67 30 Franklin
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69 new ordering "**3-1,6,4-5**" will return::
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71 26 Sager
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72 22 Peltonen-Palotie
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73 18 McClintock
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74 38 Stevens
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75 30 Franklin
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76 34 Auerbach
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77 </help>
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78 </tool>