Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/modifyGenomicCoordinates.xml @ 15:440ceca58672
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| author | m-zytnicki |
|---|---|
| date | Mon, 22 Apr 2013 11:08:07 -0400 |
| parents | 769e306b7933 |
| children | 94ab73e8a190 |
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| 14:c79b9ae3f65f | 15:440ceca58672 |
|---|---|
| 64 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | 64 <param name="inputFileName" format="gtf" type="data" label="Input File"/> |
| 65 </when> | 65 </when> |
| 66 </conditional> | 66 </conditional> |
| 67 | 67 |
| 68 <conditional name="OptionStart"> | 68 <conditional name="OptionStart"> |
| 69 <param name="start" type="select" label="restrict to the start of the transcript"> | 69 <param name="start" type="select" label="shrink to the start of the feature"> |
| 70 <option value="Yes">Yes</option> | 70 <option value="Yes">Yes</option> |
| 71 <option value="No" selected="true">No</option> | 71 <option value="No" selected="true">No</option> |
| 72 </param> | 72 </param> |
| 73 <when value="Yes"> | 73 <when value="Yes"> |
| 74 <param name="startValue" type="integer" value="0"/> | 74 <param name="startValue" type="integer" value="0"/> |
| 76 <when value="No"> | 76 <when value="No"> |
| 77 </when> | 77 </when> |
| 78 </conditional> | 78 </conditional> |
| 79 | 79 |
| 80 <conditional name="OptionEnd"> | 80 <conditional name="OptionEnd"> |
| 81 <param name="end" type="select" label="restrict to the end of the transcript"> | 81 <param name="end" type="select" label="shrink to the end of the feature"> |
| 82 <option value="Yes">Yes</option> | 82 <option value="Yes">Yes</option> |
| 83 <option value="No" selected="true">No</option> | 83 <option value="No" selected="true">No</option> |
| 84 </param> | 84 </param> |
| 85 <when value="Yes"> | 85 <when value="Yes"> |
| 86 <param name="endValue" type="integer" value="0"/> | 86 <param name="endValue" type="integer" value="0"/> |
| 120 <outputs> | 120 <outputs> |
| 121 <data format="gff3" name="outputFile" label="[modifyGenomicCoordinates] Output File"/> | 121 <data format="gff3" name="outputFile" label="[modifyGenomicCoordinates] Output File"/> |
| 122 </outputs> | 122 </outputs> |
| 123 | 123 |
| 124 <help> | 124 <help> |
| 125 This tool reads a list of transcripts and modifies each feature by: | |
| 126 | |
| 127 - shrinking it to the $ n $ first nucleotides or the *n* last nucleotides, or | |
| 128 | |
| 129 - extending it to $ n $ nucleotides towards the 5' direction (upstream) or the 3' direction (downstream). | |
| 130 | |
| 131 Note that the 5' or 3' direction depends on the orientation of the feature (the 5' end of a transcript located on the minus strand is on the right hand of this transcript!). | |
| 132 | |
| 133 The tool needs a transcript file, its format, and outputs a new transcript file. | |
| 125 </help> | 134 </help> |
| 126 </tool> | 135 </tool> |