Mercurial > repos > miller-lab > genome_diversity
comparison restore_attributes.xml @ 22:95a05c1ef5d5
update to devshed revision aaece207bd01
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Mon, 11 Mar 2013 11:28:06 -0400 |
| parents | |
| children | 91e835060ad2 |
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| 21:d6b961721037 | 22:95a05c1ef5d5 |
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| 1 <tool id="gd_restore_attributes" name="Restore Attributes" version="1.0.0"> | |
| 2 <description>: Fill in missing properties for a gd_snp dataset</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 cp.py "$dst" "$output" | |
| 6 </command> | |
| 7 | |
| 8 <inputs> | |
| 9 <param name="src" type="data" format="gd_snp" label="SNP dataset to copy attributes from" /> | |
| 10 <param name="dst" type="data" format="gd_snp" label="SNP dataset to receive attributes" /> | |
| 11 </inputs> | |
| 12 | |
| 13 <outputs> | |
| 14 <data name="output" format="gd_snp" metadata_source="src" /> | |
| 15 </outputs> | |
| 16 | |
| 17 <help> | |
| 18 | |
| 19 **Dataset formats** | |
| 20 | |
| 21 All of the input and output datasets are in gd_snp_ format. (`Dataset missing?`_) | |
| 22 | |
| 23 .. _gd_snp: ./static/formatHelp.html#gd_snp | |
| 24 .. _Dataset missing?: ./static/formatHelp.html | |
| 25 | |
| 26 ----- | |
| 27 | |
| 28 **What it does** | |
| 29 | |
| 30 This tool copies metadata information from one SNP dataset to another, leaving | |
| 31 the actual SNP data itself unchanged. Datasets in gd_snp format have a number | |
| 32 of "extra" properties associated with them, such as the focus species (which | |
| 33 may be different from the reference assembly), names of individuals, column | |
| 34 numbers containing certain data fields, etc. These values are stored in the | |
| 35 dataset's metadata, in addition to the more usual attributes like dataset name, | |
| 36 assembly build, and so forth. You can see some of these by clicking on the | |
| 37 pencil icon for the dataset. | |
| 38 | |
| 39 The Genome Diversity tools need this information to perform their tasks. | |
| 40 However, these additional attributes may be lost if the datatype is changed. | |
| 41 For example, suppose you want to see which SNPs overlap some other dataset in | |
| 42 your history, like coding regions or TAL1 binding sites. The Intersect tool | |
| 43 only works on datasets that are in interval format, so you might use the Compute | |
| 44 tool to append a new column with the End position of the SNP (= Start + 1), | |
| 45 then use the pencil icon to change the datatype to "interval". This works | |
| 46 great for doing the intersection, but if you then want to run one of the Genome | |
| 47 Diversity tools on the resulting SNPs, there's a problem: you can change the | |
| 48 datatype back to gd_snp easily enough, but the extra attributes have been lost | |
| 49 in the conversion to interval. | |
| 50 | |
| 51 As long as the proper values of the lost attributes have not changed, then this | |
| 52 tool can restore them by copying from the old gd_snp dataset in your history. | |
| 53 In the above example, appending a column does not change the numbering of the | |
| 54 earlier columns, and deleting rows via Intersect does not affect the extra | |
| 55 attributes either. Note that all of the metadata is copied, not just the extra | |
| 56 attributes specific to gd_snp (though standard items like the assembly build, | |
| 57 the number of lines, and the name for the output dataset are updated | |
| 58 automatically by the Galaxy framework). | |
| 59 | |
| 60 </help> | |
| 61 </tool> |