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comparison FeatureFinderMultiplex.xml @ 0:14e0f052de8e 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 12:37:44 -0500
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children 23d1e0b5cf9f
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-1:000000000000 0:14e0f052de8e
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: [Quantitation]-->
4 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.1.0">
5 <description>Determination of peak ratios in LC-MS data</description>
6 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FeatureFinderMultiplex
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_features:
22 -out_features $param_out_features
23 #end if
24 #if $param_out_mzq:
25 -out_mzq $param_out_mzq
26 #end if
27 #if $param_algorithm_labels:
28 -algorithm:labels "$param_algorithm_labels"
29 #end if
30 #if $param_algorithm_charge:
31 -algorithm:charge "$param_algorithm_charge"
32 #end if
33 #if $param_algorithm_rt_typical:
34 -algorithm:rt_typical $param_algorithm_rt_typical
35 #end if
36 #if $param_algorithm_rt_min:
37 -algorithm:rt_min $param_algorithm_rt_min
38 #end if
39 #if $param_algorithm_mz_tolerance:
40 -algorithm:mz_tolerance $param_algorithm_mz_tolerance
41 #end if
42 #if $param_algorithm_mz_unit:
43 -algorithm:mz_unit $param_algorithm_mz_unit
44 #end if
45 #if $param_algorithm_intensity_cutoff:
46 -algorithm:intensity_cutoff $param_algorithm_intensity_cutoff
47 #end if
48 #if $param_algorithm_peptide_similarity:
49 -algorithm:peptide_similarity $param_algorithm_peptide_similarity
50 #end if
51 #if $param_algorithm_averagine_similarity:
52 -algorithm:averagine_similarity $param_algorithm_averagine_similarity
53 #end if
54 #if $param_algorithm_missed_cleavages:
55 -algorithm:missed_cleavages $param_algorithm_missed_cleavages
56 #end if
57 #if $adv_opts.adv_opts_selector=='advanced':
58 #if $adv_opts.param_force:
59 -force
60 #end if
61 #if $adv_opts.param_algorithm_isotopes_per_peptide:
62 -algorithm:isotopes_per_peptide "$adv_opts.param_algorithm_isotopes_per_peptide"
63 #end if
64 #if $adv_opts.param_algorithm_averagine_similarity_scaling:
65 -algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling
66 #end if
67 #if $adv_opts.param_algorithm_knock_out:
68 -algorithm:knock_out
69 #end if
70 #if $adv_opts.param_algorithm_averagine_type:
71 -algorithm:averagine_type $adv_opts.param_algorithm_averagine_type
72 #end if
73 #if $adv_opts.param_labels_Arg6:
74 -labels:Arg6 $adv_opts.param_labels_Arg6
75 #end if
76 #if $adv_opts.param_labels_Arg10:
77 -labels:Arg10 $adv_opts.param_labels_Arg10
78 #end if
79 #if $adv_opts.param_labels_Lys4:
80 -labels:Lys4 $adv_opts.param_labels_Lys4
81 #end if
82 #if $adv_opts.param_labels_Lys6:
83 -labels:Lys6 $adv_opts.param_labels_Lys6
84 #end if
85 #if $adv_opts.param_labels_Lys8:
86 -labels:Lys8 $adv_opts.param_labels_Lys8
87 #end if
88 #if $adv_opts.param_labels_Leu3:
89 -labels:Leu3 $adv_opts.param_labels_Leu3
90 #end if
91 #if $adv_opts.param_labels_Dimethyl0:
92 -labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0
93 #end if
94 #if $adv_opts.param_labels_Dimethyl4:
95 -labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4
96 #end if
97 #if $adv_opts.param_labels_Dimethyl6:
98 -labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6
99 #end if
100 #if $adv_opts.param_labels_Dimethyl8:
101 -labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8
102 #end if
103 #if $adv_opts.param_labels_ICPL0:
104 -labels:ICPL0 $adv_opts.param_labels_ICPL0
105 #end if
106 #if $adv_opts.param_labels_ICPL4:
107 -labels:ICPL4 $adv_opts.param_labels_ICPL4
108 #end if
109 #if $adv_opts.param_labels_ICPL6:
110 -labels:ICPL6 $adv_opts.param_labels_ICPL6
111 #end if
112 #if $adv_opts.param_labels_ICPL10:
113 -labels:ICPL10 $adv_opts.param_labels_ICPL10
114 #end if
115 #end if
116 </command>
117 <inputs>
118 <param name="param_in" type="data" format="mzml" optional="False" label="LC-MS dataset in centroid or profile mode" help="(-in) "/>
119 <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">
120 <sanitizer>
121 <valid initial="string.printable">
122 <remove value="'"/>
123 <remove value="&quot;"/>
124 </valid>
125 </sanitizer>
126 </param>
127 <param name="param_algorithm_charge" type="text" size="30" value="1:4" label="Range of charge states in the sample, i.e" help="(-charge) min charge : max charge">
128 <sanitizer>
129 <valid initial="string.printable">
130 <remove value="'"/>
131 <remove value="&quot;"/>
132 </valid>
133 </sanitizer>
134 </param>
135 <param name="param_algorithm_rt_typical" type="float" min="0.0" optional="True" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes" help="(-rt_typical) (This is not an upper bound. Peptides that elute for longer will be reported.)"/>
136 <param name="param_algorithm_rt_min" type="float" min="0.0" optional="True" value="2.0" label="Lower bound for the retention time [s]" help="(-rt_min) (Any peptides seen for a shorter time period are not reported.)"/>
137 <param name="param_algorithm_mz_tolerance" type="float" min="0.0" optional="True" value="6.0" label="m/z tolerance for search of peak patterns" help="(-mz_tolerance) "/>
138 <param name="param_algorithm_mz_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of the 'mz_tolerance' paramete" help="(-mz_unit) ">
139 <option value="Da">Da</option>
140 <option value="ppm" selected="true">ppm</option>
141 </param>
142 <param name="param_algorithm_intensity_cutoff" type="float" min="0.0" optional="True" value="1000.0" label="Lower bound for the intensity of isotopic peaks" help="(-intensity_cutoff) "/>
143 <param name="param_algorithm_peptide_similarity" type="float" min="-1.0" max="1.0" optional="True" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern" help="(-peptide_similarity) This parameter is a lower bound on their similarity"/>
144 <param name="param_algorithm_averagine_similarity" type="float" min="-1.0" max="1.0" optional="True" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" help="(-averagine_similarity) This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/>
145 <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.)"/>
146 <expand macro="advanced_options">
147 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
148 <param name="param_algorithm_isotopes_per_peptide" type="text" size="30" value="3:6" label="Range of isotopes per peptide in the sample" help="(-isotopes_per_peptide) For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. ">
149 <sanitizer>
150 <valid initial="string.printable">
151 <remove value="'"/>
152 <remove value="&quot;"/>
153 </valid>
154 </sanitizer>
155 </param>
156 <param name="param_algorithm_averagine_similarity_scaling" type="float" min="0.0" max="1.0" optional="True" value="0.75" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="(-averagine_similarity_scaling) For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/>
157 <param name="param_algorithm_knock_out" display="radio" type="boolean" truevalue="-algorithm:knock_out" falsevalue="" checked="false" optional="True" label="Is it likely that knock-outs are present?" help="(-knock_out) (Supported for doublex, triplex and quadruplex experiments only.)"/>
158 <param name="param_algorithm_averagine_type" display="radio" type="select" optional="False" value="peptide" label="The type of averagine to use, currently RNA, DNA or peptide" help="(-averagine_type) ">
159 <option value="peptide" selected="true">peptide</option>
160 <option value="RNA">RNA</option>
161 <option value="DNA">DNA</option>
162 </param>
163 <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) "/>
164 <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) "/>
165 <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) "/>
166 <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) "/>
167 <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) "/>
168 <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) "/>
169 <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) "/>
170 <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) "/>
171 <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) "/>
172 <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) "/>
173 <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) "/>
174 <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) "/>
175 <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) "/>
176 <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) "/>
177 </expand>
178 </inputs>
179 <outputs>
180 <data name="param_out" format="consensusxml"/>
181 <data name="param_out_features" format="featurexml"/>
182 <data name="param_out_mzq" format="mzq"/>
183 </outputs>
184 <help>Determination of peak ratios in LC-MS data
185
186
187 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMultiplex.html</help>
188 </tool>