[2] | 1 | <tool id="EMBOSS: pepcoil68" name="pepcoil" version="5.0.0">
|
---|
| 2 | <description>Predicts coiled coil regions</description>
|
---|
| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
---|
| 4 | <command>pepcoil -sequence $input1 -outfile $out_file1 -window $window -coil $coil -frame $frame -other $other -auto</command>
|
---|
| 5 | <inputs>
|
---|
| 6 | <param format="data" name="input1" type="data">
|
---|
| 7 | <label>Sequence</label>
|
---|
| 8 | </param>
|
---|
| 9 | <param name="window" size="4" type="text" value="28">
|
---|
| 10 | <label>Window size</label>
|
---|
| 11 | </param>
|
---|
| 12 | <param name="coil" type="select">
|
---|
| 13 | <label>Report coiled coil regions</label>
|
---|
| 14 | <option value="yes">Yes</option>
|
---|
| 15 | <option value="no">No</option>
|
---|
| 16 | </param>
|
---|
| 17 | <param name="frame" type="select">
|
---|
| 18 | <label>Show coil frameshifts</label>
|
---|
| 19 | <option value="yes">Yes</option>
|
---|
| 20 | <option value="no">No</option>
|
---|
| 21 | </param>
|
---|
| 22 | <param name="other" type="select">
|
---|
| 23 | <label>Report non coiled coil regions</label>
|
---|
| 24 | <option value="yes">Yes</option>
|
---|
| 25 | <option value="no">No</option>
|
---|
| 26 | </param>
|
---|
| 27 | </inputs>
|
---|
| 28 | <outputs>
|
---|
| 29 | <data format="pepcoil" name="out_file1" />
|
---|
| 30 | </outputs> |
---|
| 31 | <tests> |
---|
| 32 | <test> |
---|
| 33 | <param name="input1" value="2.fasta"/> |
---|
| 34 | <param name="window" value="28"/> |
---|
| 35 | <param name="coil" value="yes"/> |
---|
| 36 | <param name="frame" value="yes"/> |
---|
| 37 | <param name="other" value="yes"/> |
---|
| 38 | <output name="out_file1" file="emboss_pepcoil_out.pepcoil"/> |
---|
| 39 | </test> |
---|
| 40 | </tests>
|
---|
| 41 | <help> |
---|
| 42 | You can view the original documentation here_. |
---|
| 43 | |
---|
| 44 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepcoil.html |
---|
| 45 | </help> |
---|
| 46 | </tool> |
---|