Mercurial > repos > bgruening > openms

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
3 <!--Proposed Tool Section: [Targeted Experiments]-->
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
4 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="2.0.0">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
5 <description>Generates decoys according to different models for a specific TraML</description>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
6 <macros>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
7 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
8 <import>macros.xml</import>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
9 </macros>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
10 <expand macro="references"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
11 <expand macro="stdio"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
12 <expand macro="requirements"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
13 <command>OpenSwathDecoyGenerator
0
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
14
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
15 #if $param_in:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
16 -in $param_in
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
17 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
18 #if $param_out:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
19 -out $param_out
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
20 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
21 #if $param_method:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
22 -method &quot;$param_method&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
23 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
24 #if $param_decoy_tag:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
25 -decoy_tag &quot;$param_decoy_tag&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
26 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
27 #if $param_theoretical:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
28 -theoretical
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
29 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
30 #if $param_mz_threshold:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
31 -mz_threshold $param_mz_threshold
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
32 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
33 #if $param_exclude_similar:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
34 -exclude_similar
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
35 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
36 #if $param_similarity_threshold:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
37 -similarity_threshold $param_similarity_threshold
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
38 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
39 #if $param_append:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
40 -append
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
41 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
42 #if $param_remove_CNterm_mods:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
43 -remove_CNterm_mods
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
44 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
45 #if $param_remove_unannotated:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
46 -remove_unannotated
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
47 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
48 #if $param_enable_losses:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
49 -enable_losses
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
50 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
51 #if $param_identity_threshold:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
52 -identity_threshold $param_identity_threshold
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
53 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
54 #if $param_max_attempts:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
55 -max_attempts $param_max_attempts
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
56 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
57 #if $param_mz_shift:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
58 -mz_shift $param_mz_shift
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
59 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
60 #if $param_precursor_mass_shift:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
61 -precursor_mass_shift $param_precursor_mass_shift
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
62 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
63 -threads \${GALAXY_SLOTS:-24}
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
64 #if $adv_opts.adv_opts_selector=='advanced':
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
65 #if $adv_opts.param_force:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
66 -force
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
67 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
68 #end if
0
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
69 </command>
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
70 <inputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
71 <param format="traml" help="(-in) " label="input file ('traML')" name="param_in" optional="False" type="data"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
72 <param help="(-method) " label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" name="param_method" size="30" type="text" value="shuffle">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
73 <sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
74 <valid initial="string.printable">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
75 <remove value="'"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
76 <remove value="&quot;"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
77 </valid>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
78 </sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
79 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
80 <param help="(-decoy_tag) " label="decoy tag" name="param_decoy_tag" size="30" type="text" value="DECOY_">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
81 <sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
82 <valid initial="string.printable">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
83 <remove value="'"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
84 <remove value="&quot;"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
85 </valid>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
86 </sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
87 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
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"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
89 <param help="(-mz_threshold) " label="MZ threshold in Thomson for fragment ion annotation" name="param_mz_threshold" type="float" value="0.05"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
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"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
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"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
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"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
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"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
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"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
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"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
96 <param help="(-identity_threshold) " label="shuffle: identity threshold for the shuffle algorithm" name="param_identity_threshold" type="float" value="0.7"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
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"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
98 <param help="(-mz_shift) " label="shift: MZ shift in Thomson for shift decoy method" name="param_mz_shift" type="float" value="20.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
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"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
100 <expand macro="advanced_options">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
101 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
102 </expand>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
103 </inputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
104 <outputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
105 <data format="traml" name="param_out"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
106 </outputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
107 <help>Generates decoys according to different models for a specific TraML
0
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
108
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
109
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
110 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDecoyGenerator.html</help>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
111 </tool>