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annotate restore_attributes.xml @ 24:248b06e86022

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Added gd_genotype datatype. Modified tools to support new datatype.
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 28 May 2013 16:24:19 -0400
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children 91e835060ad2
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1 <tool id="gd_restore_attributes" name="Restore Attributes" version="1.0.0">
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2 <description>: Fill in missing properties for a gd_snp 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 <param name="src" type="data" format="gd_snp" label="SNP dataset to copy attributes from" />
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10 <param name="dst" type="data" format="gd_snp" label="SNP dataset to receive attributes" />
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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_snp" metadata_source="src" />
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15 </outputs>
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16
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17 <help>
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18
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19 **Dataset formats**
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20
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21 All of the input and output datasets are in gd_snp_ format. (`Dataset missing?`_)
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22
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23 .. _gd_snp: ./static/formatHelp.html#gd_snp
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24 .. _Dataset missing?: ./static/formatHelp.html
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25
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26 -----
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27
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28 **What it does**
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29
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30 This tool copies metadata information from one SNP dataset to another, leaving
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31 the actual SNP data itself unchanged. Datasets in gd_snp format have a number
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32 of "extra" properties associated with them, such as the focus species (which
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33 may be different from the reference assembly), names of individuals, column
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34 numbers containing certain data fields, etc. These values are stored in the
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35 dataset's metadata, in addition to the more usual attributes like dataset name,
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36 assembly build, and so forth. You can see some of these by clicking on the
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37 pencil icon for the dataset.
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38
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39 The Genome Diversity tools need this information to perform their tasks.
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40 However, these additional attributes may be lost if the datatype is changed.
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41 For example, suppose you want to see which SNPs overlap some other dataset in
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42 your history, like coding regions or TAL1 binding sites. The Intersect tool
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43 only works on datasets that are in interval format, so you might use the Compute
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44 tool to append a new column with the End position of the SNP (= Start + 1),
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45 then use the pencil icon to change the datatype to "interval". This works
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46 great for doing the intersection, but if you then want to run one of the Genome
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47 Diversity tools on the resulting SNPs, there's a problem: you can change the
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48 datatype back to gd_snp easily enough, but the extra attributes have been lost
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49 in the conversion to interval.
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50
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51 As long as the proper values of the lost attributes have not changed, then this
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52 tool can restore them by copying from the old gd_snp dataset in your history.
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53 In the above example, appending a column does not change the numbering of the
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54 earlier columns, and deleting rows via Intersect does not affect the extra
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55 attributes either. Note that all of the metadata is copied, not just the extra
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56 attributes specific to gd_snp (though standard items like the assembly build,
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57 the number of lines, and the name for the output dataset are updated
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58 automatically by the Galaxy framework).
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59
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60 </help>
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61 </tool>