Mercurial > repos > bgruening > diamond
comparison diamand.xml @ 2:09a565cfc192 draft
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 07 Feb 2015 12:19:45 -0500 |
| parents | fbe4eedec466 |
| children | e1326442d13f |
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| 1:fbe4eedec466 | 2:09a565cfc192 |
|---|---|
| 45 $salltitles | 45 $salltitles |
| 46 | 46 |
| 47 ]]> | 47 ]]> |
| 48 </command> | 48 </command> |
| 49 <inputs> | 49 <inputs> |
| 50 <conditional name="method"> | |
| 51 <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)"> | |
| 52 <option value="blastp">Align amino acid query sequences (blastp)</option> | |
| 53 <option value="blastx">Align DNA query sequences (blastx)</option> | |
| 54 </param> | |
| 55 <when value="blastp"> | |
| 56 <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" /> | |
| 57 <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" /> | |
| 58 </when> | |
| 59 <when value="blastx"> | |
| 60 <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" /> | |
| 61 <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" /> | |
| 62 </when> | |
| 63 </conditional> | |
| 64 | 50 |
| 65 <param name="query" type="data" format="fasta" label="Input query file in FASTA format" /> | 51 <param name="query" type="data" format="fasta" label="Input query file in FASTA format" /> |
| 66 | 52 |
| 67 <conditional name="ref_db_source"> | 53 <conditional name="ref_db_source"> |
| 68 <param name="db_source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> | 54 <param name="db_source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> |
| 81 </param> | 67 </param> |
| 82 </when> <!-- build-in --> | 68 </when> <!-- build-in --> |
| 83 <when value="history"> | 69 <when value="history"> |
| 84 <param name="reference_database" type="data" format="compressed_archive" label="Select the reference database" /> | 70 <param name="reference_database" type="data" format="compressed_archive" label="Select the reference database" /> |
| 85 </when> <!-- history --> | 71 </when> <!-- history --> |
| 72 </conditional> | |
| 73 | |
| 74 <conditional name="method"> | |
| 75 <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)"> | |
| 76 <option value="blastp">Align amino acid query sequences (blastp)</option> | |
| 77 <option value="blastx">Align DNA query sequences (blastx)</option> | |
| 78 </param> | |
| 79 <when value="blastp"> | |
| 80 <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" /> | |
| 81 <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" /> | |
| 82 </when> | |
| 83 <when value="blastx"> | |
| 84 <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" /> | |
| 85 <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" /> | |
| 86 </when> | |
| 86 </conditional> | 87 </conditional> |
| 87 | 88 |
| 88 <param name="matrix" type="select" label="Select scoring matrix" help="(--matrix)"> | 89 <param name="matrix" type="select" label="Select scoring matrix" help="(--matrix)"> |
| 89 <option value="BLOSUM45">BLOSUM45</option> | 90 <option value="BLOSUM45">BLOSUM45</option> |
| 90 <option value="BLOSUM50">BLOSUM50</option> | 91 <option value="BLOSUM50">BLOSUM50</option> |