Mercurial > repos > peterjc > get_orfs_or_cdss
comparison tools/get_orfs_or_cdss/get_orfs_or_cdss.xml @ 9:a06ad07431ba draft
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
| author | peterjc |
|---|---|
| date | Wed, 10 May 2017 13:24:46 -0400 |
| parents | 09a8be9247ca |
| children | 01b0488d9cfb |
comparison
equal
deleted
inserted
replaced
| 8:09a8be9247ca | 9:a06ad07431ba |
|---|---|
| 1 <tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.0"> | 1 <tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.1"> |
| 2 <description>e.g. to get peptides from ESTs</description> | 2 <description>e.g. to get peptides from ESTs</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.65">biopython</requirement> | 4 <requirement type="package" version="1.67">biopython</requirement> |
| 5 <requirement type="python-module">Bio</requirement> | |
| 6 </requirements> | 5 </requirements> |
| 7 <stdio> | 6 <stdio> |
| 8 <!-- Anything other than zero is an error --> | 7 <!-- Anything other than zero is an error --> |
| 9 <exit_code range="1:" /> | 8 <exit_code range="1:" /> |
| 10 <exit_code range=":-1" /> | 9 <exit_code range=":-1" /> |
| 32 <option value="16">16. Chlorophycean Mitochondrial</option> | 31 <option value="16">16. Chlorophycean Mitochondrial</option> |
| 33 <option value="21">21. Trematode Mitochondrial</option> | 32 <option value="21">21. Trematode Mitochondrial</option> |
| 34 <option value="22">22. Scenedesmus obliquus</option> | 33 <option value="22">22. Scenedesmus obliquus</option> |
| 35 <option value="23">23. Thraustochytrium Mitochondrial</option> | 34 <option value="23">23. Thraustochytrium Mitochondrial</option> |
| 36 <option value="24">24. Pterobranchia Mitochondrial</option> | 35 <option value="24">24. Pterobranchia Mitochondrial</option> |
| 36 <option value="25">25. Candidate Division SR1 and Gracilibacteria</option> | |
| 37 <!-- TODO, these are not in Biopython 1.67 | |
| 38 <option value="26">26. Pachysolen tannophilus Nuclear</option> | |
| 39 <option value="26">27. Karyorelict Nuclear</option> | |
| 40 <option value="26">28. Condylostoma Nuclear</option> | |
| 41 <option value="26">29. Mesodinium Nuclear</option> | |
| 42 <option value="26">30. Peritrich Nuclear</option> | |
| 43 <option value="26">31. Blastocrithidia Nuclear</option> | |
| 44 --> | |
| 37 </param> | 45 </param> |
| 38 <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs"> | 46 <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs"> |
| 39 <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option> | 47 <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option> |
| 40 <option value="CDS">Look for CDSs (with start and stop codons)</option> | 48 <option value="CDS">Look for CDSs (with start and stop codons)</option> |
| 41 </param> | 49 </param> |