Mercurial > repos > bgruening > deeptools
comparison deepTools_macros.xml @ 38:9afae9d021cd draft
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 01 Feb 2014 06:12:38 -0500 |
| parents | 2f7edf06a5da |
| children | 20f8dafb554f |
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| 37:2f7edf06a5da | 38:9afae9d021cd |
|---|---|
| 185 <conditional name="effectiveGenomeSize"> | 185 <conditional name="effectiveGenomeSize"> |
| 186 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" | 186 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" |
| 187 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. | 187 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. |
| 188 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. | 188 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. |
| 189 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes."> | 189 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes."> |
| 190 <option value="93260000">ce10 (93260000)</option> | |
| 191 <option value="121400000">dm3 (121400000)</option> | |
| 192 <option value="2451960000" selected="true">hg19 (2451960000)</option> | |
| 190 <option value="2150570000">mm9 (2150570000)</option> | 193 <option value="2150570000">mm9 (2150570000)</option> |
| 191 <option value="2451960000">hg19 (2451960000)</option> | |
| 192 <option value="121400000">dm3 (121400000)</option> | |
| 193 <option value="93260000">ce10 (93260000)</option> | |
| 194 <option value="specific">user specified</option> | 194 <option value="specific">user specified</option> |
| 195 </param> | 195 </param> |
| 196 <when value="specific"> | 196 <when value="specific"> |
| 197 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" /> | 197 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" /> |
| 198 </when> | 198 </when> |
| 199 <when value="2150570000" /> | |
| 200 <when value="2451960000" /> | |
| 201 <when value="121400000" /> | |
| 202 <when value="93260000" /> | |
| 199 </conditional> | 203 </conditional> |
| 200 </xml> | 204 </xml> |
| 201 | 205 |
| 202 <xml name="image_file_format"> | 206 <xml name="image_file_format"> |
| 203 <param name="outFileFormat" type="select" label="Image file format"> | 207 <param name="outFileFormat" type="select" label="Image file format"> |