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comparison OpenSwathDecoyGenerator.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="1.12.0"> 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 <description>Generates decoys according to different models for a specific TraML</description> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <macros> 4 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="2.0.0">
5 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token> 5 <description>Generates decoys according to different models for a specific TraML</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>OpenSwathDecoyGenerator 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathDecoyGenerator
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -method ${param_method} 17 #end if
15 -decoy_tag ${param_decoy_tag} 18 #if $param_out:
16 ${param_theoretical} 19 -out $param_out
17 -mz_threshold ${param_mz_threshold} 20 #end if
18 ${param_exclude_similar} 21 #if $param_method:
19 -similarity_threshold ${param_similarity_threshold} 22 -method &quot;$param_method&quot;
20 ${param_append} 23 #end if
21 ${param_remove_CNterm_mods} 24 #if $param_decoy_tag:
22 ${param_remove_unannotated} 25 -decoy_tag &quot;$param_decoy_tag&quot;
23 ${param_enable_losses} 26 #end if
24 -identity_threshold ${param_identity_threshold} 27 #if $param_theoretical:
25 -max_attempts ${param_max_attempts} 28 -theoretical
26 -mz_shift ${param_mz_shift} 29 #end if
27 -precursor_mass_shift ${param_precursor_mass_shift} 30 #if $param_mz_threshold:
28 -threads \${GALAXY_SLOTS:-24} 31 -mz_threshold $param_mz_threshold
32 #end if
33 #if $param_exclude_similar:
34 -exclude_similar
35 #end if
36 #if $param_similarity_threshold:
37 -similarity_threshold $param_similarity_threshold
38 #end if
39 #if $param_append:
40 -append
41 #end if
42 #if $param_remove_CNterm_mods:
43 -remove_CNterm_mods
44 #end if
45 #if $param_remove_unannotated:
46 -remove_unannotated
47 #end if
48 #if $param_enable_losses:
49 -enable_losses
50 #end if
51 #if $param_identity_threshold:
52 -identity_threshold $param_identity_threshold
53 #end if
54 #if $param_max_attempts:
55 -max_attempts $param_max_attempts
56 #end if
57 #if $param_mz_shift:
58 -mz_shift $param_mz_shift
59 #end if
60 #if $param_precursor_mass_shift:
61 -precursor_mass_shift $param_precursor_mass_shift
62 #end if
63 -threads \${GALAXY_SLOTS:-24}
64 #if $adv_opts.adv_opts_selector=='advanced':
65 #if $adv_opts.param_force:
66 -force
67 #end if
68 #end if
29 </command> 69 </command>
30 <inputs> 70 <inputs>
31 <param name="param_in" type="data" format="" optional="False" label="input file ('traML')" help="(-in)"/> 71 <param format="traml" help="(-in) " label="input file ('traML')" name="param_in" optional="False" type="data"/>
32 <param name="param_method" type="text" size="20" value="shuffle" label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" help="(-method)"/> 72 <param help="(-method) " label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" name="param_method" size="30" type="text" value="shuffle">
33 <param name="param_decoy_tag" type="text" size="20" value="DECOY_" label="decoy tag" help="(-decoy_tag)"/> 73 <sanitizer>
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)"/> 74 <valid initial="string.printable">
35 <param name="param_mz_threshold" type="float" value="0.05" label="MZ threshold in Thomson for fragment ion annotation" help="(-mz_threshold)"/> 75 <remove value="'"/>
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)"/> 76 <remove value="&quot;"/>
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)"/> 77 </valid>
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)"/> 78 </sanitizer>
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)"/> 79 </param>
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)"/> 80 <param help="(-decoy_tag) " label="decoy tag" name="param_decoy_tag" size="30" type="text" value="DECOY_">
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)"/> 81 <sanitizer>
42 <param name="param_identity_threshold" type="float" value="0.7" label="shuffle: identity threshold for the shuffle algorithm" help="(-identity_threshold)"/> 82 <valid initial="string.printable">
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)"/> 83 <remove value="'"/>
44 <param name="param_mz_shift" type="float" value="20.0" label="shift: MZ shift in Thomson for shift decoy method" help="(-mz_shift)"/> 84 <remove value="&quot;"/>
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)"/> 85 </valid>
46 </inputs> 86 </sanitizer>
47 <outputs> 87 </param>
48 <data name="param_out" label="output file" format="data"/> 88 <param checked="false" falsevalue="" help="(-theoretical) " label="set this flag if only annotated transitions should be used and be corrected to the theoretical mz" name="param_theoretical" optional="True" truevalue="-theoretical" type="boolean"/>
49 </outputs> 89 <param help="(-mz_threshold) " label="MZ threshold in Thomson for fragment ion annotation" name="param_mz_threshold" type="float" value="0.05"/>
50 <help>**What it does** 90 <param checked="false" falsevalue="" 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" 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" name="param_exclude_similar" optional="True" truevalue="-exclude_similar" type="boolean"/>
51 91 <param help="(-similarity_threshold) Suggested value: 0.05" label="Similarity threshold for absolute difference of the product mz of target and decoy assays for exclusion in Dalton" name="param_similarity_threshold" type="float" value="-1.0"/>
52 Generates decoys according to different models for a specific TraML 92 <param checked="false" falsevalue="" help="(-append) " label="set this flag if non-decoy TraML should be appended to the output" name="param_append" optional="True" truevalue="-append" type="boolean"/>
93 <param checked="false" falsevalue="" help="(-remove_CNterm_mods) " label="set this flag to remove decoy peptides with C/N terminal modifications (may be necessary depending on the decoy generation method)" name="param_remove_CNterm_mods" optional="True" truevalue="-remove_CNterm_mods" type="boolean"/>
94 <param checked="false" falsevalue="" help="(-remove_unannotated) " label="set this flag if target assays with unannotated ions should be ignored from decoy generation" name="param_remove_unannotated" optional="True" truevalue="-remove_unannotated" type="boolean"/>
95 <param checked="false" falsevalue="" help="(-enable_losses) " label="set this flag if fragment ions should also be annotated with neutral losses" name="param_enable_losses" optional="True" truevalue="-enable_losses" type="boolean"/>
96 <param help="(-identity_threshold) " label="shuffle: identity threshold for the shuffle algorithm" name="param_identity_threshold" type="float" value="0.7"/>
97 <param help="(-max_attempts) " label="shuffle: maximum attempts to lower the sequence identity between target and decoy for the shuffle algorithm" name="param_max_attempts" type="integer" value="10"/>
98 <param help="(-mz_shift) " label="shift: MZ shift in Thomson for shift decoy method" name="param_mz_shift" type="float" value="20.0"/>
99 <param help="(-precursor_mass_shift) " label="Mass shift to apply to the precursor ion" name="param_precursor_mass_shift" type="float" value="0.0"/>
100 <expand macro="advanced_options">
101 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
102 </expand>
103 </inputs>
104 <outputs>
105 <data format="traml" name="param_out"/>
106 </outputs>
107 <help>Generates decoys according to different models for a specific TraML
53 108
54 109
55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDecoyGenerator.html 110 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDecoyGenerator.html</help>
56 111 </tool>
57 @REFERENCES@
58 </help>
59 </tool>