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comparison MultiplexResolver.xml @ 0:6e272bce9aa1 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 12:49:31 -0500
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children 7268379f9860
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-1:000000000000 0:6e272bce9aa1
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: [Utilities]-->
4 <tool id="MultiplexResolver" name="MultiplexResolver" version="2.1.0">
5 <description>Completes peptide multiplets and resolves conflicts within them.</description>
6 <macros>
7 <token name="@EXECUTABLE@">MultiplexResolver</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MultiplexResolver
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_out_conflicts:
22 -out_conflicts $param_out_conflicts
23 #end if
24 #if $param_algorithm_labels:
25 -algorithm:labels "$param_algorithm_labels"
26 #end if
27 #if $param_algorithm_missed_cleavages:
28 -algorithm:missed_cleavages $param_algorithm_missed_cleavages
29 #end if
30 #if $adv_opts.adv_opts_selector=='advanced':
31 #if $adv_opts.param_force:
32 -force
33 #end if
34 #if $adv_opts.param_algorithm_mass_tolerance:
35 -algorithm:mass_tolerance $adv_opts.param_algorithm_mass_tolerance
36 #end if
37 #if $adv_opts.param_labels_Arg6:
38 -labels:Arg6 $adv_opts.param_labels_Arg6
39 #end if
40 #if $adv_opts.param_labels_Arg10:
41 -labels:Arg10 $adv_opts.param_labels_Arg10
42 #end if
43 #if $adv_opts.param_labels_Lys4:
44 -labels:Lys4 $adv_opts.param_labels_Lys4
45 #end if
46 #if $adv_opts.param_labels_Lys6:
47 -labels:Lys6 $adv_opts.param_labels_Lys6
48 #end if
49 #if $adv_opts.param_labels_Lys8:
50 -labels:Lys8 $adv_opts.param_labels_Lys8
51 #end if
52 #if $adv_opts.param_labels_Leu3:
53 -labels:Leu3 $adv_opts.param_labels_Leu3
54 #end if
55 #if $adv_opts.param_labels_Dimethyl0:
56 -labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0
57 #end if
58 #if $adv_opts.param_labels_Dimethyl4:
59 -labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4
60 #end if
61 #if $adv_opts.param_labels_Dimethyl6:
62 -labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6
63 #end if
64 #if $adv_opts.param_labels_Dimethyl8:
65 -labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8
66 #end if
67 #if $adv_opts.param_labels_ICPL0:
68 -labels:ICPL0 $adv_opts.param_labels_ICPL0
69 #end if
70 #if $adv_opts.param_labels_ICPL4:
71 -labels:ICPL4 $adv_opts.param_labels_ICPL4
72 #end if
73 #if $adv_opts.param_labels_ICPL6:
74 -labels:ICPL6 $adv_opts.param_labels_ICPL6
75 #end if
76 #if $adv_opts.param_labels_ICPL10:
77 -labels:ICPL10 $adv_opts.param_labels_ICPL10
78 #end if
79 #end if
80 </command>
81 <inputs>
82 <param name="param_in" type="data" format="consensusxml" optional="False" label="Peptide multiplets with assigned sequence information" help="(-in) "/>
83 <param name="param_algorithm_labels" type="text" size="30" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="(-labels) [...] specifies the labels for a single sample. For example &lt;br&gt; &lt;br&gt;[][Lys8,Arg10] ... SILAC &lt;br&gt;[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC &lt;br&gt;[Dimethyl0][Dimethyl6] ... Dimethyl &lt;br&gt;[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl &lt;br&gt;[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL">
84 <sanitizer>
85 <valid initial="string.printable">
86 <remove value="'"/>
87 <remove value="&quot;"/>
88 </valid>
89 </sanitizer>
90 </param>
91 <param name="param_algorithm_missed_cleavages" type="integer" min="0" optional="True" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(-missed_cleavages) (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
92 <expand macro="advanced_options">
93 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
94 <param name="param_algorithm_mass_tolerance" type="float" value="0.1" label="Mass tolerance in Da for matching the detected to the theoretical mass shifts" help="(-mass_tolerance) "/>
95 <param name="param_labels_Arg6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help="(-Arg6) "/>
96 <param name="param_labels_Arg10" type="float" min="0.0" optional="True" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help="(-Arg10) "/>
97 <param name="param_labels_Lys4" type="float" min="0.0" optional="True" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help="(-Lys4) "/>
98 <param name="param_labels_Lys6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help="(-Lys6) "/>
99 <param name="param_labels_Lys8" type="float" min="0.0" optional="True" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help="(-Lys8) "/>
100 <param name="param_labels_Leu3" type="float" min="0.0" optional="True" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help="(-Leu3) "/>
101 <param name="param_labels_Dimethyl0" type="float" min="0.0" optional="True" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help="(-Dimethyl0) "/>
102 <param name="param_labels_Dimethyl4" type="float" min="0.0" optional="True" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help="(-Dimethyl4) "/>
103 <param name="param_labels_Dimethyl6" type="float" min="0.0" optional="True" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help="(-Dimethyl6) "/>
104 <param name="param_labels_Dimethyl8" type="float" min="0.0" optional="True" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help="(-Dimethyl8) "/>
105 <param name="param_labels_ICPL0" type="float" min="0.0" optional="True" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help="(-ICPL0) "/>
106 <param name="param_labels_ICPL4" type="float" min="0.0" optional="True" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help="(-ICPL4) "/>
107 <param name="param_labels_ICPL6" type="float" min="0.0" optional="True" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help="(-ICPL6) "/>
108 <param name="param_labels_ICPL10" type="float" min="0.0" optional="True" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help="(-ICPL10) "/>
109 </expand>
110 </inputs>
111 <outputs>
112 <data name="param_out" format="consensusxml"/>
113 <data name="param_out_conflicts" format="consensusxml"/>
114 </outputs>
115 <help>Completes peptide multiplets and resolves conflicts within them.
116
117
118 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MultiplexResolver.html</help>
119 </tool>