Mercurial > repos > iracooke > msgfplus
comparison msgfplus_search.xml @ 12:49231acb2258 draft
Uploaded
| author | iracooke |
|---|---|
| date | Wed, 25 Jun 2014 19:00:11 -0400 |
| parents | deb61a965680 |
| children | c1df871ffa3c |
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| 11:deb61a965680 | 12:49231acb2258 |
|---|---|
| 44 --max-pep-len=$max_pep_len | 44 --max-pep-len=$max_pep_len |
| 45 --max-pep-charge=$max_pep_charge | 45 --max-pep-charge=$max_pep_charge |
| 46 --min-pep-charge=$min_pep_charge | 46 --min-pep-charge=$min_pep_charge |
| 47 --num-reported-matches=$num_reported_matches | 47 --num-reported-matches=$num_reported_matches |
| 48 --java-mem=$java_mem | 48 --java-mem=$java_mem |
| 49 #unless $pepxml_output_use: | 49 #if $pepxml_output_use: |
| 50 --no-pepxml | 50 --pepxml |
| 51 #end unless | 51 #end unless |
| 52 </command> | 52 </command> |
| 53 | 53 |
| 54 <inputs> | 54 <inputs> |
| 55 <conditional name="database"> | 55 <conditional name="database"> |
| 101 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue="" /> | 101 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue="" /> |
| 102 | 102 |
| 103 <param name="enzyme" type="select" format="text"> | 103 <param name="enzyme" type="select" format="text"> |
| 104 <label>Enzyme</label> | 104 <label>Enzyme</label> |
| 105 <option value="0">unspecific cleavage</option> | 105 <option value="0">unspecific cleavage</option> |
| 106 <option value="1">Trypsin</option> | 106 <option value="1" selected="true">Trypsin</option> |
| 107 <option value="2">Chymotrypsin</option> | 107 <option value="2">Chymotrypsin</option> |
| 108 <option value="3">Lys-C</option> | 108 <option value="3">Lys-C</option> |
| 109 <option value="4">Lys-N</option> | 109 <option value="4">Lys-N</option> |
| 110 <option value="5">glutamyl endopeptidase</option> | 110 <option value="5">glutamyl endopeptidase</option> |
| 111 <option value="6">Arg-C</option> | 111 <option value="6">Arg-C</option> |