|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="1.12.0">
|
|
|
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 -in ${param_in}
|
|
|
13 -out ${param_out}
|
|
|
14 -method ${param_method}
|
|
|
15 -decoy_tag ${param_decoy_tag}
|
|
|
16 ${param_theoretical}
|
|
|
17 -mz_threshold ${param_mz_threshold}
|
|
|
18 ${param_exclude_similar}
|
|
|
19 -similarity_threshold ${param_similarity_threshold}
|
|
|
20 ${param_append}
|
|
|
21 ${param_remove_CNterm_mods}
|
|
|
22 ${param_remove_unannotated}
|
|
|
23 ${param_enable_losses}
|
|
|
24 -identity_threshold ${param_identity_threshold}
|
|
|
25 -max_attempts ${param_max_attempts}
|
|
|
26 -mz_shift ${param_mz_shift}
|
|
|
27 -precursor_mass_shift ${param_precursor_mass_shift}
|
|
|
28 -threads \${GALAXY_SLOTS:-24}
|
|
|
29 </command>
|
|
|
30 <inputs>
|
|
|
31 <param name="param_in" type="data" format="" optional="False" label="input file ('traML')" help="(-in)"/>
|
|
|
32 <param name="param_method" type="text" size="20" value="shuffle" label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" help="(-method)"/>
|
|
|
33 <param name="param_decoy_tag" type="text" size="20" value="DECOY_" label="decoy tag" help="(-decoy_tag)"/>
|
|
|
34 <param name="param_theoretical" type="boolean" truevalue="-theoretical true" falsevalue="-theoretical false" checked="false" optional="True" label="set this flag if only annotated transitions should be used and be corrected to the theoretical mz." help="(-theoretical)"/>
|
|
|
35 <param name="param_mz_threshold" type="float" value="0.05" label="MZ threshold in Thomson for fragment ion annotation" help="(-mz_threshold)"/>
|
|
|
36 <param name="param_exclude_similar" type="boolean" truevalue="-exclude_similar true" falsevalue="-exclude_similar false" 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. 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." help="(-exclude_similar)"/>
|
|
|
37 <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. Suggested value: 0.05" help="(-similarity_threshold)"/>
|
|
|
38 <param name="param_append" type="boolean" truevalue="-append true" falsevalue="-append false" checked="false" optional="True" label="set this flag if non-decoy TraML should be appended to the output." help="(-append)"/>
|
|
|
39 <param name="param_remove_CNterm_mods" type="boolean" truevalue="-remove_CNterm_mods true" falsevalue="-remove_CNterm_mods false" 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)"/>
|
|
|
40 <param name="param_remove_unannotated" type="boolean" truevalue="-remove_unannotated true" falsevalue="-remove_unannotated false" checked="false" optional="True" label="set this flag if target assays with unannotated ions should be ignored from decoy generation." help="(-remove_unannotated)"/>
|
|
|
41 <param name="param_enable_losses" type="boolean" truevalue="-enable_losses true" falsevalue="-enable_losses false" checked="false" optional="True" label="set this flag if fragment ions should also be annotated with neutral losses." help="(-enable_losses)"/>
|
|
|
42 <param name="param_identity_threshold" type="float" value="0.7" label="shuffle: identity threshold for the shuffle algorithm" help="(-identity_threshold)"/>
|
|
|
43 <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)"/>
|
|
|
44 <param name="param_mz_shift" type="float" value="20.0" label="shift: MZ shift in Thomson for shift decoy method" help="(-mz_shift)"/>
|
|
|
45 <param name="param_precursor_mass_shift" type="float" value="0.0" label="Mass shift to apply to the precursor ion" help="(-precursor_mass_shift)"/>
|
|
|
46 </inputs>
|
|
|
47 <outputs>
|
|
|
48 <data name="param_out" label="output file" format="data"/>
|
|
|
49 </outputs>
|
|
|
50 <help>**What it does**
|
|
|
51
|
|
|
52 Generates decoys according to different models for a specific TraML
|
|
|
53
|
|
|
54
|
|
|
55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDecoyGenerator.html
|
|
|
56
|
|
|
57 @REFERENCES@
|
|
|
58 </help>
|
|
|
59 </tool>
|
