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comparison OpenSwathDecoyGenerator.xml @ 0:d38ef9cbc114 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:44:50 -0500
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children 659ba0ad1cfd
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-1:000000000000 0:d38ef9cbc114
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="2.1.0">
5 <description>Generates decoys according to different models for a specific TraML</description>
6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathDecoyGenerator
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_method:
22 -method "$param_method"
23 #end if
24 #if $param_decoy_tag:
25 -decoy_tag "$param_decoy_tag"
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_identity_threshold:
46 -identity_threshold $param_identity_threshold
47 #end if
48 #if $param_max_attempts:
49 -max_attempts $param_max_attempts
50 #end if
51 #if $param_mz_shift:
52 -mz_shift $param_mz_shift
53 #end if
54 #if $param_precursor_mass_shift:
55 -precursor_mass_shift $param_precursor_mass_shift
56 #end if
57 #if $param_allowed_fragment_types:
58 -allowed_fragment_types "$param_allowed_fragment_types"
59 #end if
60 #if $param_allowed_fragment_charges:
61 -allowed_fragment_charges "$param_allowed_fragment_charges"
62 #end if
63 #if $param_enable_detection_specific_losses:
64 -enable_detection_specific_losses
65 #end if
66 #if $param_enable_detection_unspecific_losses:
67 -enable_detection_unspecific_losses
68 #end if
69 #if $adv_opts.adv_opts_selector=='advanced':
70 #if $adv_opts.param_force:
71 -force
72 #end if
73 #end if
74 </command>
75 <inputs>
76 <param name="param_in" type="data" format="traml" optional="False" label="input file ('traML')" help="(-in) "/>
77 <param name="param_method" type="text" size="30" value="shuffle" label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" help="(-method) ">
78 <sanitizer>
79 <valid initial="string.printable">
80 <remove value="'"/>
81 <remove value="&quot;"/>
82 </valid>
83 </sanitizer>
84 </param>
85 <param name="param_decoy_tag" type="text" size="30" value="DECOY_" label="decoy tag" help="(-decoy_tag) ">
86 <sanitizer>
87 <valid initial="string.printable">
88 <remove value="'"/>
89 <remove value="&quot;"/>
90 </valid>
91 </sanitizer>
92 </param>
93 <param name="param_mz_threshold" type="float" value="0.05" label="MZ threshold in Thomson for fragment ion annotation" help="(-mz_threshold) "/>
94 <param name="param_exclude_similar" display="radio" 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"/>
95 <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"/>
96 <param name="param_append" display="radio" 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) "/>
97 <param name="param_remove_CNterm_mods" display="radio" 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) "/>
98 <param name="param_remove_unannotated" display="radio" 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) "/>
99 <param name="param_identity_threshold" type="float" value="0.7" label="shuffle: identity threshold for the shuffle algorithm" help="(-identity_threshold) "/>
100 <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) "/>
101 <param name="param_mz_shift" type="float" value="20.0" label="shift: MZ shift in Thomson for shift decoy method" help="(-mz_shift) "/>
102 <param name="param_precursor_mass_shift" type="float" value="0.0" label="Mass shift to apply to the precursor ion" help="(-precursor_mass_shift) "/>
103 <param name="param_allowed_fragment_types" type="text" size="30" value="b,y" label="allowed fragment types" help="(-allowed_fragment_types) ">
104 <sanitizer>
105 <valid initial="string.printable">
106 <remove value="'"/>
107 <remove value="&quot;"/>
108 </valid>
109 </sanitizer>
110 </param>
111 <param name="param_allowed_fragment_charges" type="text" size="30" value="1,2,3,4" label="allowed fragment charge states" help="(-allowed_fragment_charges) ">
112 <sanitizer>
113 <valid initial="string.printable">
114 <remove value="'"/>
115 <remove value="&quot;"/>
116 </valid>
117 </sanitizer>
118 </param>
119 <param name="param_enable_detection_specific_losses" display="radio" type="boolean" truevalue="-enable_detection_specific_losses" falsevalue="" checked="false" optional="True" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help="(-enable_detection_specific_losses) "/>
120 <param name="param_enable_detection_unspecific_losses" display="radio" type="boolean" truevalue="-enable_detection_unspecific_losses" falsevalue="" checked="false" optional="True" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help="(-enable_detection_unspecific_losses) "/>
121 <expand macro="advanced_options">
122 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
123 </expand>
124 </inputs>
125 <outputs>
126 <data name="param_out" format="traml"/>
127 </outputs>
128 <help>Generates decoys according to different models for a specific TraML
129
130
131 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDecoyGenerator.html</help>
132 </tool>