|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.0.0">
|
|
|
3 <description>Determination of peak ratios in LC-MS data</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>FeatureFinderMultiplex
|
|
|
11
|
|
|
12 #if $param_in:
|
|
|
13 -in $param_in
|
|
|
14 #end if
|
|
|
15 #if $param_out:
|
|
|
16 -out $param_out
|
|
|
17 #end if
|
|
|
18 #if $param_out_features:
|
|
|
19 -out_features $param_out_features
|
|
|
20 #end if
|
|
|
21 #if $param_out_mzq:
|
|
|
22 -out_mzq $param_out_mzq
|
|
|
23 #end if
|
|
|
24 -threads \${GALAXY_SLOTS:-24}
|
|
|
25 #if $param_algorithm_labels:
|
|
|
26 -algorithm:labels "$param_algorithm_labels"
|
|
|
27 #end if
|
|
|
28 #if $param_algorithm_charge:
|
|
|
29 -algorithm:charge "$param_algorithm_charge"
|
|
|
30 #end if
|
|
|
31 #if $param_algorithm_rt_typical:
|
|
|
32 -algorithm:rt_typical $param_algorithm_rt_typical
|
|
|
33 #end if
|
|
|
34 #if $param_algorithm_rt_min:
|
|
|
35 -algorithm:rt_min $param_algorithm_rt_min
|
|
|
36 #end if
|
|
|
37 #if $param_algorithm_mz_tolerance:
|
|
|
38 -algorithm:mz_tolerance $param_algorithm_mz_tolerance
|
|
|
39 #end if
|
|
|
40 #if $param_algorithm_mz_unit:
|
|
|
41 -algorithm:mz_unit
|
|
|
42 #if " " in str($param_algorithm_mz_unit):
|
|
|
43 "$param_algorithm_mz_unit"
|
|
|
44 #else
|
|
|
45 $param_algorithm_mz_unit
|
|
|
46 #end if
|
|
|
47 #end if
|
|
|
48 #if $param_algorithm_intensity_cutoff:
|
|
|
49 -algorithm:intensity_cutoff $param_algorithm_intensity_cutoff
|
|
|
50 #end if
|
|
|
51 #if $param_algorithm_peptide_similarity:
|
|
|
52 -algorithm:peptide_similarity $param_algorithm_peptide_similarity
|
|
|
53 #end if
|
|
|
54 #if $param_algorithm_averagine_similarity:
|
|
|
55 -algorithm:averagine_similarity $param_algorithm_averagine_similarity
|
|
|
56 #end if
|
|
|
57 #if $param_algorithm_missed_cleavages:
|
|
|
58 -algorithm:missed_cleavages $param_algorithm_missed_cleavages
|
|
|
59 #end if
|
|
|
60 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
61 #if $adv_opts.param_force:
|
|
|
62 -force
|
|
|
63 #end if
|
|
|
64 #if $adv_opts.param_algorithm_isotopes_per_peptide:
|
|
|
65 -algorithm:isotopes_per_peptide "$adv_opts.param_algorithm_isotopes_per_peptide"
|
|
|
66 #end if
|
|
|
67 #if $adv_opts.param_algorithm_averagine_similarity_scaling:
|
|
|
68 -algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling
|
|
|
69 #end if
|
|
|
70 #if $adv_opts.param_algorithm_knock_out:
|
|
|
71 -algorithm:knock_out
|
|
|
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_Dimethyl0:
|
|
|
89 -labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0
|
|
|
90 #end if
|
|
|
91 #if $adv_opts.param_labels_Dimethyl4:
|
|
|
92 -labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4
|
|
|
93 #end if
|
|
|
94 #if $adv_opts.param_labels_Dimethyl6:
|
|
|
95 -labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6
|
|
|
96 #end if
|
|
|
97 #if $adv_opts.param_labels_Dimethyl8:
|
|
|
98 -labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8
|
|
|
99 #end if
|
|
|
100 #if $adv_opts.param_labels_ICPL0:
|
|
|
101 -labels:ICPL0 $adv_opts.param_labels_ICPL0
|
|
|
102 #end if
|
|
|
103 #if $adv_opts.param_labels_ICPL4:
|
|
|
104 -labels:ICPL4 $adv_opts.param_labels_ICPL4
|
|
|
105 #end if
|
|
|
106 #if $adv_opts.param_labels_ICPL6:
|
|
|
107 -labels:ICPL6 $adv_opts.param_labels_ICPL6
|
|
|
108 #end if
|
|
|
109 #if $adv_opts.param_labels_ICPL10:
|
|
|
110 -labels:ICPL10 $adv_opts.param_labels_ICPL10
|
|
|
111 #end if
|
|
|
112 #end if
|
|
|
113 </command>
|
|
|
114 <inputs>
|
|
|
115 <param name="param_in" type="data" format="mzml" optional="False" label="LC-MS dataset in centroid or profile mode" help="(-in) "/>
|
|
|
116 <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 <br> <br>[][Lys8,Arg10] ... SILAC <br>[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC <br>[Dimethyl0][Dimethyl6] ... Dimethyl <br>[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl <br>[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL">
|
|
|
117 <sanitizer>
|
|
|
118 <valid initial="string.printable">
|
|
|
119 <remove value="'"/>
|
|
|
120 <remove value="""/>
|
|
|
121 </valid>
|
|
|
122 </sanitizer>
|
|
|
123 </param>
|
|
|
124 <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">
|
|
|
125 <sanitizer>
|
|
|
126 <valid initial="string.printable">
|
|
|
127 <remove value="'"/>
|
|
|
128 <remove value="""/>
|
|
|
129 </valid>
|
|
|
130 </sanitizer>
|
|
|
131 </param>
|
|
|
132 <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.)"/>
|
|
|
133 <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.)"/>
|
|
|
134 <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) "/>
|
|
|
135 <param name="param_algorithm_mz_unit" type="select" optional="True" value="ppm" label="Unit of the 'mz_tolerance' paramete" help="(-mz_unit) ">
|
|
|
136 <option value="Da">Da</option>
|
|
|
137 <option value="ppm">ppm</option>
|
|
|
138 </param>
|
|
|
139 <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) "/>
|
|
|
140 <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"/>
|
|
|
141 <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"/>
|
|
|
142 <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) "/>
|
|
|
143 <expand macro="advanced_options">
|
|
|
144 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
145 <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. ">
|
|
|
146 <sanitizer>
|
|
|
147 <valid initial="string.printable">
|
|
|
148 <remove value="'"/>
|
|
|
149 <remove value="""/>
|
|
|
150 </valid>
|
|
|
151 </sanitizer>
|
|
|
152 </param>
|
|
|
153 <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 -> p' = p and x = 1 -> 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.)"/>
|
|
|
154 <param name="param_algorithm_knock_out" 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.)"/>
|
|
|
155 <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) "/>
|
|
|
156 <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) "/>
|
|
|
157 <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) "/>
|
|
|
158 <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) "/>
|
|
|
159 <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) "/>
|
|
|
160 <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) "/>
|
|
|
161 <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) "/>
|
|
|
162 <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) "/>
|
|
|
163 <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) "/>
|
|
|
164 <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) "/>
|
|
|
165 <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) "/>
|
|
|
166 <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) "/>
|
|
|
167 <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) "/>
|
|
|
168 </expand>
|
|
|
169 </inputs>
|
|
|
170 <outputs>
|
|
|
171 <data name="param_out" format="consensusxml"/>
|
|
|
172 <data name="param_out_features" format="featurexml"/>
|
|
|
173 <data name="param_out_mzq" format="mzq"/>
|
|
|
174 </outputs>
|
|
|
175 <help>**What it does**
|
|
|
176
|
|
|
177 Determination of peak ratios in LC-MS data
|
|
|
178
|
|
|
179
|
|
|
180 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMultiplex.html</help>
|
|
|
181 <expand macro="references"/>
|
|
|
182 </tool>
|
