Mercurial > repos > iracooke > msgfplus

comparison msgfplus_search.xml @ 13:c1df871ffa3c draft

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Uploaded
author iracooke
date Wed, 25 Jun 2014 23:03:32 -0400
parents 49231acb2258
children 32365fec702c
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12:49231acb2258 13:c1df871ffa3c
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 $cleavage_semi
37 -f $fragment_ion_tol
38 -p $precursor_ion_tol 37 -p $precursor_ion_tol
39 --instrument=$instrument 38 --instrument=$instrument
40 --isotope-error-range=$isotope_error_range 39 --isotope-error-range=$isotope_error_range
41 --fragment-method=$fragment_method 40 --fragment-method=$fragment_method
42 --protocol=$protocol 41 --protocol=$protocol
46 --min-pep-charge=$min_pep_charge 45 --min-pep-charge=$min_pep_charge
47 --num-reported-matches=$num_reported_matches 46 --num-reported-matches=$num_reported_matches
48 --java-mem=$java_mem 47 --java-mem=$java_mem
49 #if $pepxml_output_use: 48 #if $pepxml_output_use:
50 --pepxml 49 --pepxml
51 #end unless 50 #end if
52 </command> 51 </command>
53 52
54 <inputs> 53 <inputs>
55 <conditional name="database"> 54 <conditional name="database">
56 <param name="source_select" type="select" label="Database source"> 55 <param name="source_select" type="select" label="Database source">
68 </when> 67 </when>
69 <when value="input_ref"> 68 <when value="input_ref">
70 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> 69 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
71 </when> 70 </when>
72 </conditional> 71 </conditional>
73 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/> 72 <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
74 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed"> 73 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
75 <options from_file="msgfplus_mods.loc"> 74 <options from_file="msgfplus_mods.loc">
76 <column name="name" index="0" /> 75 <column name="name" index="0" />
77 <column name="value" index="2" /> 76 <column name="value" index="2" />
78 </options> 77 </options>
136 <option value="1">Phosphorylation</option> 135 <option value="1">Phosphorylation</option>
137 <option value="2">iTRAQ</option> 136 <option value="2">iTRAQ</option>
138 <option value="3">iTRAQPhospho</option> 137 <option value="3">iTRAQPhospho</option>
139 </param> 138 </param>
140 139
141 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
142
143 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/> 140 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
144 <param name="precursor_tolu" type="select" format="text"> 141 <param name="precursor_tolu" type="select" format="text">
145 <label>Precursor Ion Tolerance Units</label> 142 <label>Precursor Ion Tolerance Units</label>
146 <option value="ppm">ppm</option> 143 <option value="ppm">ppm</option>
147 <option value="Da">Da</option> 144 <option value="Da">Da</option>