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Bug fixes for Draw variants, Phylip, and gd_d_tools
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 13:46:10 -0500
parents 91e835060ad2
children
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1 <tool id="gd_restore_attributes" name="Restore Attributes" version="1.1.0">
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2 <description>: Fill in missing properties for a gd_snp or gd_genotype dataset</description>
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3
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4 <command interpreter="python">
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5 cp.py "$dst" "$output"
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6 </command>
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7
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8 <inputs>
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9 <conditional name="input_type">
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10 <param name="choice" type="select" format="integer" label="Input format">
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11 <option value="0" selected="true">gd_snp</option>
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12 <option value="1">gd_genotype</option>
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13 </param>
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14
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15 <when value="0">
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16 <param name="input" type="data" format="gd_snp" label="SNP dataset to copy attributes from" />
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17 <param name="dst" type="data" format="gd_snp" label="SNP dataset to receive attributes" />
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18 </when>
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19 <when value="1">
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20 <param name="input" type="data" format="gd_genotype" label="Genotype dataset to copy attributes from" />
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21 <param name="dst" type="data" format="gd_genotype" label="Genotype dataset to receive attributes" />
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22 </when>
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23 </conditional>
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24 </inputs>
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25
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26 <outputs>
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27 <data name="output" format="input" format_source="input" metadata_source="input" />
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28 </outputs>
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29
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30 <help>
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31
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32 **Dataset formats**
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33
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34 All of the input and output datasets are in gd_snp_ or gd_genotype_ format. (`Dataset missing?`_)
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36 .. _gd_snp: ./static/formatHelp.html#gd_snp
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37 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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38 .. _Dataset missing?: ./static/formatHelp.html
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39
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40 -----
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41
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42 **What it does**
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43
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44 This tool copies metadata information from one SNP dataset to another, leaving
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45 the actual SNP data itself unchanged. Datasets in gd_snp format have a number
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46 of "extra" properties associated with them, such as the focus species (which
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47 may be different from the reference assembly), names of individuals, column
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48 numbers containing certain data fields, etc. These values are stored in the
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49 dataset's metadata, in addition to the more usual attributes like dataset name,
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50 assembly build, and so forth. You can see some of these by clicking on the
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51 pencil icon for the dataset.
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52
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53 The Genome Diversity tools need this information to perform their tasks.
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54 However, these additional attributes may be lost if the datatype is changed.
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55 For example, suppose you want to see which SNPs overlap some other dataset in
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56 your history, like coding regions or TAL1 binding sites. The Intersect tool
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57 only works on datasets that are in interval format, so you might use the Compute
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58 tool to append a new column with the End position of the SNP (= Start + 1),
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59 then use the pencil icon to change the datatype to "interval". This works
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60 great for doing the intersection, but if you then want to run one of the Genome
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61 Diversity tools on the resulting SNPs, there's a problem: you can change the
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62 datatype back to gd_snp easily enough, but the extra attributes have been lost
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63 in the conversion to interval.
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64
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65 As long as the proper values of the lost attributes have not changed, then this
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66 tool can restore them by copying from the old gd_snp dataset in your history.
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67 In the above example, appending a column does not change the numbering of the
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68 earlier columns, and deleting rows via Intersect does not affect the extra
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69 attributes either. Note that all of the metadata is copied, not just the extra
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70 attributes specific to gd_snp (though standard items like the assembly build,
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71 the number of lines, and the name for the output dataset are updated
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72 automatically by the Galaxy framework).
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73
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74 </help>
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75 </tool>