Mercurial > repos > iracooke > msgfplus

comparison msgfplus_search.xml @ 12:49231acb2258 draft

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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>