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comparison msgfplus_search.xml @ 6:79ed4588f7ae draft

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author iracooke
date Tue, 18 Mar 2014 19:46:10 -0400
parents 233ce0ebad08
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5:233ce0ebad08 6:79ed4588f7ae
1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.1"> 1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.2">
2 <description>Run an MSGF+ Search</description> 2 <description>Run an MSGF+ Search</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.6">protk</requirement> 4 <requirement type="package" version="1.2.6">protk</requirement>
5 <requirement type="package" version="20140210">msgfplus</requirement> 5 <requirement type="package" version="20140210">msgfplus</requirement>
6 <requirement type="package" version="3_0_4388">proteowizard</requirement> 6 <requirement type="package" version="3_0_4388">proteowizard</requirement>
30 $input_file 30 $input_file
31 -o $output 31 -o $output
32 -r 32 -r
33 --enzyme=$enzyme 33 --enzyme=$enzyme
34 --precursor-ion-tol-units=$precursor_tolu 34 --precursor-ion-tol-units=$precursor_tolu
35 -v $missed_cleavages 35 -v $missed_cleavages
36 $cleavage_semi
36 -f $fragment_ion_tol 37 -f $fragment_ion_tol
37 -p $precursor_ion_tol 38 -p $precursor_ion_tol
38 --instrument=$instrument 39 --instrument=$instrument
39 --isotope-error-range=$isotope_error_range 40 --isotope-error-range=$isotope_error_range
40 --fragment-method=$fragment_method 41 --fragment-method=$fragment_method
95 <option value="0">0</option> 96 <option value="0">0</option>
96 <option value="1">1</option> 97 <option value="1">1</option>
97 <option value="2">2</option> 98 <option value="2">2</option>
98 </param> 99 </param>
99 100
101 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="" falsevalue="--no-cleavage-semi" />
102
100 <param name="enzyme" type="select" format="text"> 103 <param name="enzyme" type="select" format="text">
101 <label>Enzyme</label> 104 <label>Enzyme</label>
102 <option value="0">unspecific cleavage</option> 105 <option value="0">unspecific cleavage</option>
103 <option value="1">Trypsin</option> 106 <option value="1">Trypsin</option>
104 <option value="2">Chymotrypsin</option> 107 <option value="2">Chymotrypsin</option>