|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="2.0.0">
|
|
|
3 <description>Generates decoys according to different models for a specific TraML</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>OpenSwathDecoyGenerator
|
|
|
11
|
|
|
12 #if $param_in:
|
|
|
13 -in $param_in
|
|
|
14 #end if
|
|
|
15 #if $param_out:
|
|
|
16 -out $param_out
|
|
|
17 #end if
|
|
|
18 #if $param_method:
|
|
|
19 -method "$param_method"
|
|
|
20 #end if
|
|
|
21 #if $param_decoy_tag:
|
|
|
22 -decoy_tag "$param_decoy_tag"
|
|
|
23 #end if
|
|
|
24 #if $param_theoretical:
|
|
|
25 -theoretical
|
|
|
26 #end if
|
|
|
27 #if $param_mz_threshold:
|
|
|
28 -mz_threshold $param_mz_threshold
|
|
|
29 #end if
|
|
|
30 #if $param_exclude_similar:
|
|
|
31 -exclude_similar
|
|
|
32 #end if
|
|
|
33 #if $param_similarity_threshold:
|
|
|
34 -similarity_threshold $param_similarity_threshold
|
|
|
35 #end if
|
|
|
36 #if $param_append:
|
|
|
37 -append
|
|
|
38 #end if
|
|
|
39 #if $param_remove_CNterm_mods:
|
|
|
40 -remove_CNterm_mods
|
|
|
41 #end if
|
|
|
42 #if $param_remove_unannotated:
|
|
|
43 -remove_unannotated
|
|
|
44 #end if
|
|
|
45 #if $param_enable_losses:
|
|
|
46 -enable_losses
|
|
|
47 #end if
|
|
|
48 #if $param_identity_threshold:
|
|
|
49 -identity_threshold $param_identity_threshold
|
|
|
50 #end if
|
|
|
51 #if $param_max_attempts:
|
|
|
52 -max_attempts $param_max_attempts
|
|
|
53 #end if
|
|
|
54 #if $param_mz_shift:
|
|
|
55 -mz_shift $param_mz_shift
|
|
|
56 #end if
|
|
|
57 #if $param_precursor_mass_shift:
|
|
|
58 -precursor_mass_shift $param_precursor_mass_shift
|
|
|
59 #end if
|
|
|
60 -threads \${GALAXY_SLOTS:-24}
|
|
|
61 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
62 #if $adv_opts.param_force:
|
|
|
63 -force
|
|
|
64 #end if
|
|
|
65 #end if
|
|
|
66 </command>
|
|
|
67 <inputs>
|
|
|
68 <param name="param_in" type="data" format="traml" optional="False" label="input file ('traML')" help="(-in) "/>
|
|
|
69 <param name="param_method" type="text" size="30" value="shuffle" label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" help="(-method) ">
|
|
|
70 <sanitizer>
|
|
|
71 <valid initial="string.printable">
|
|
|
72 <remove value="'"/>
|
|
|
73 <remove value="""/>
|
|
|
74 </valid>
|
|
|
75 </sanitizer>
|
|
|
76 </param>
|
|
|
77 <param name="param_decoy_tag" type="text" size="30" value="DECOY_" label="decoy tag" help="(-decoy_tag) ">
|
|
|
78 <sanitizer>
|
|
|
79 <valid initial="string.printable">
|
|
|
80 <remove value="'"/>
|
|
|
81 <remove value="""/>
|
|
|
82 </valid>
|
|
|
83 </sanitizer>
|
|
|
84 </param>
|
|
|
85 <param name="param_theoretical" type="boolean" truevalue="-theoretical" falsevalue="" checked="false" optional="True" label="set this flag if only annotated transitions should be used and be corrected to the theoretical mz" help="(-theoretical) "/>
|
|
|
86 <param name="param_mz_threshold" type="float" value="0.05" label="MZ threshold in Thomson for fragment ion annotation" help="(-mz_threshold) "/>
|
|
|
87 <param name="param_exclude_similar" type="boolean" truevalue="-exclude_similar" falsevalue="" checked="false" optional="True" label="set this flag if decoy assays with similarity of the peptide sequence to the target assays higher than the identity_threshold should be excluded" help="(-exclude_similar) If similarity_threshold is over 0, decoy assays with an absolute difference of the decoy and target product mz smaller than similarity_threshold are further excluded"/>
|
|
|
88 <param name="param_similarity_threshold" type="float" value="-1.0" label="Similarity threshold for absolute difference of the product mz of target and decoy assays for exclusion in Dalton" help="(-similarity_threshold) Suggested value: 0.05"/>
|
|
|
89 <param name="param_append" type="boolean" truevalue="-append" falsevalue="" checked="false" optional="True" label="set this flag if non-decoy TraML should be appended to the output" help="(-append) "/>
|
|
|
90 <param name="param_remove_CNterm_mods" type="boolean" truevalue="-remove_CNterm_mods" falsevalue="" checked="false" optional="True" label="set this flag to remove decoy peptides with C/N terminal modifications (may be necessary depending on the decoy generation method)" help="(-remove_CNterm_mods) "/>
|
|
|
91 <param name="param_remove_unannotated" type="boolean" truevalue="-remove_unannotated" falsevalue="" checked="false" optional="True" label="set this flag if target assays with unannotated ions should be ignored from decoy generation" help="(-remove_unannotated) "/>
|
|
|
92 <param name="param_enable_losses" type="boolean" truevalue="-enable_losses" falsevalue="" checked="false" optional="True" label="set this flag if fragment ions should also be annotated with neutral losses" help="(-enable_losses) "/>
|
|
|
93 <param name="param_identity_threshold" type="float" value="0.7" label="shuffle: identity threshold for the shuffle algorithm" help="(-identity_threshold) "/>
|
|
|
94 <param name="param_max_attempts" type="integer" value="10" label="shuffle: maximum attempts to lower the sequence identity between target and decoy for the shuffle algorithm" help="(-max_attempts) "/>
|
|
|
95 <param name="param_mz_shift" type="float" value="20.0" label="shift: MZ shift in Thomson for shift decoy method" help="(-mz_shift) "/>
|
|
|
96 <param name="param_precursor_mass_shift" type="float" value="0.0" label="Mass shift to apply to the precursor ion" help="(-precursor_mass_shift) "/>
|
|
|
97 <expand macro="advanced_options">
|
|
|
98 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
99 </expand>
|
|
|
100 </inputs>
|
|
|
101 <outputs>
|
|
|
102 <data name="param_out" format="traml"/>
|
|
|
103 </outputs>
|
|
|
104 <help>**What it does**
|
|
|
105
|
|
|
106 Generates decoys according to different models for a specific TraML
|
|
|
107
|
|
|
108
|
|
|
109 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDecoyGenerator.html</help>
|
|
|
110 <expand macro="references"/>
|
|
|
111 </tool>
|
