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comparison tandem.xml @ 11:618d74240c7f draft

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author iracooke
date Mon, 16 Jun 2014 05:47:55 -0400
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10:ffd1d25b8080 11:618d74240c7f
1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.2">
2
3 <requirements>
4 <requirement type="package" version="1.3.0">protk</requirement>
5 </requirements>
6
7 <description>Run an X!Tandem Search</description>
8
9 <command>
10 #if $database.source_select=="built_in":
11 tandem_search.rb -d $database.dbkey
12 #else
13 tandem_search.rb -d $database.fasta_file
14 #end if
15
16 #if $tandem_params.source_select=="built_in":
17 -T $tandem_params.paramskey
18 #else
19 -T $tandem_params.params_file
20 #end if
21
22
23 --var-mods='
24 $variable_mods
25 #for $custom_variable_mod in $custom_variable_mods:
26 ,${custom_variable_mod.custom_mod}
27 #end for
28 '
29
30 --fix-mods='
31 $fixed_mods
32 #for $custom_fix_mod in $custom_fix_mods:
33 ,${custom_fix_mod.custom_mod}
34 #end for
35 '
36
37 $input_file -o $output -r
38
39 --enzyme=$enzyme
40
41 --precursor-ion-tol-units=$precursor_tolu
42
43 -v $missed_cleavages
44
45 -f $fragment_ion_tol
46
47 -p $precursor_ion_tol
48
49 $allow_multi_isotope_search
50
51 $acetyl_protein_nterm
52
53 $cleavage_semi
54
55 $keep_spectra
56
57 --threads $threads
58
59 </command>
60
61 <inputs>
62 <conditional name="database">
63 <param name="source_select" type="select" label="Database source">
64 <option value="built_in">Built-In</option>
65 <option value="input_ref" selected="true">Your Upload File</option>
66 </param>
67 <when value="built_in">
68 <param name="dbkey" type="select" format="text" >
69 <label>Database</label>
70 <options from_file="pepxml_databases.loc">
71 <column name="name" index="0" />
72 <column name="value" index="2" />
73 </options>
74 </param>
75 </when>
76 <when value="input_ref">
77 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
78 </when>
79 </conditional>
80
81 <conditional name="tandem_params">
82 <param name="source_select" type="select" label="Baseline Parameters">
83 <option value="built_in" selected="true">Built-In</option>
84 <option value="input_ref">Custom parameter file</option>
85 </param>
86 <when value="built_in">
87 <param name="paramskey" type="select" format="text" >
88 <label>Paramset</label>
89 <option value="isb_native">ISB Native</option>
90 <option value="isb_kscore">ISB K-Score</option>
91 </param>
92 </when>
93 <when value="input_ref">
94 <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
95 </when>
96 </conditional>
97
98 <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A file with MS/MS data"/>
99
100 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
101 clicking to select multiple items">
102 <options from_file="tandem_mods.loc">
103 <column name="name" index="0" />
104 <column name="value" index="2" />
105 </options>
106 </param>
107
108 <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
109 <param name="custom_mod" type="text">
110 </param>
111 </repeat>
112
113
114 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
115 clicking to select multiple items">
116 <options from_file="tandem_mods.loc">
117 <column name="name" index="0" />
118 <column name="value" index="2" />
119 </options>
120 </param>
121
122 <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
123 <param name="custom_mod" type="text">
124 </param>
125 </repeat>
126
127 <param name="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" />
128
129
130 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
131 <label>Missed Cleavages Allowed</label>
132 <option value="0">0</option>
133 <option value="1">1</option>
134 <option value="2">2</option>
135 </param>
136
137 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/>
138
139 <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>
140
141 <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/>
142
143 <param name="enzyme" type="select" format="text">
144 <label>Enzyme</label>
145 <option value="[R]|{P}">argc - [R]|{P}</option>
146 <option value="[X]|[D]">aspn - [X]|[D]</option>
147 <option value="[FLMWY]|{P}">chymotrypsin - [FLMWY]|{P}</option>
148 <option value="[R]|[X]">clostripain - [R]|[X]</option>
149 <option value="[M]|{P}">cnbr - [M]|{P}</option>
150 <option value="[AGILV]|{P}">elastase - [AGILV]|{P}</option>
151 <option value="[D]|{P}">formicacid - [D]|{P}</option>
152 <option value="[DE]|{P}">gluc - [DE]|{P}</option>
153 <option value="[E]|{P}">gluc_bicarb - [E]|{P}</option>
154 <option value="[W]|[X]">iodosobenzoate - [W]|[X]</option>
155 <option value="[K]|{P}">lysc - [K]|{P}</option>
156 <option value="[K]|[X]">lysc-p - [K]|[X]</option>
157 <option value="[X]|[K]">lysn - [X]|[K]</option>
158 <option value="[X]|[AKRS]">lysn_promisc - [X]|[AKRS]</option>
159 <option value="[X]|[X]">nonspecific - [X]|[X]</option>
160 <option value="[FL]|[X]">pepsina - [FL]|[X]</option>
161 <option value="[P]|[X]">protein_endopeptidase - [P]|[X]</option>
162 <option value="[E]|[X]">staph_protease - [E]|[X]</option>
163 <option value="[FMWY]|{P},[KR]|{P},[X]|[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
164 <option value="[KR]|{P}" selected="true">trypsin - [KR]|{P}</option>
165 <option value="[FKLMRWY]|{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
166 <option value="[KR]|{P},[M]|{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
167 <option value="[DEKR]|{P}">trypsin_gluc - [DEKR]|{P}</option>
168 </param>
169
170
171 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
172
173 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
174 <param name="precursor_tolu" type="select" format="text">
175 <label>Precursor Ion Tolerance Units</label>
176 <option value="ppm">ppm</option>
177 <option value="Da">Da</option>
178 </param>
179
180 <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="" falsevalue=""/>
181
182 </inputs>
183
184
185 <outputs>
186 <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/>
187 </outputs>
188
189
190 <help>
191
192 **What it does**
193
194 Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
195
196 ----
197
198 **References**
199
200 Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
201
202 </help>
203
204 </tool>