Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/plotCoverage.xml @ 15:440ceca58672
Uploaded
| author | m-zytnicki |
|---|---|
| date | Mon, 22 Apr 2013 11:08:07 -0400 |
| parents | 769e306b7933 |
| children | 94ab73e8a190 |
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| 14:c79b9ae3f65f | 15:440ceca58672 |
|---|---|
| 167 <when value="No"> | 167 <when value="No"> |
| 168 </when> | 168 </when> |
| 169 </conditional> | 169 </conditional> |
| 170 | 170 |
| 171 <conditional name="optiontitle"> | 171 <conditional name="optiontitle"> |
| 172 <param name="title" type="select" label="title of the plots "> | 172 <param name="title" type="select" label="title for the figure"> |
| 173 <option value="Yes">Yes</option> | 173 <option value="Yes">Yes</option> |
| 174 <option value="No" selected="true">No</option> | 174 <option value="No" selected="true">No</option> |
| 175 </param> | 175 </param> |
| 176 <when value="Yes"> | 176 <when value="Yes"> |
| 177 <param name="titleVal" type="text" value=" " /> | 177 <param name="titleVal" type="text" value=" " /> |
| 258 <outputs> | 258 <outputs> |
| 259 <data name="outputFile" format="tar" label="[plotCoverage] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/> | 259 <data name="outputFile" format="tar" label="[plotCoverage] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/> |
| 260 </outputs> | 260 </outputs> |
| 261 | 261 |
| 262 <help> | 262 <help> |
| 263 This script gives a .tar out file, if you want to take look at the results, you have to download it. | 263 Plot the coverage of the first set of genomic coordinates with respect to the second set of genomic coordinates. For each element of the second set (we will suppose that they are annotated genes), it computes the number of elements of the first set (reads, for instance) which overlap it. |
| 264 | |
| 265 Alternatively, if the first file is in GFF format, and contains the **Target** file, you can omit the second file. However, a fasta file corresponding to the second file should be given (to compute the size of the reference elements). | |
| 266 | |
| 267 The tool produces two plots per gene. The first plot gives the coverage: a point (*x*, *y*) $ means that *y* reads cover the *x*th nucleotide of the gene. The second figure displays the (possibly spliced) gene in black, and the overlapping reads (blue is colinear, red is anti-sense). | |
| 268 | |
| 269 This script gives a .tar out file, if you want to take look at the results, you have to download it. | |
| 264 </help> | 270 </help> |
| 265 </tool> | 271 </tool> |