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comparison FeatureFinderMultiplex.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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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 &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">
117 <sanitizer>
118 <valid initial="string.printable">
119 <remove value="'"/>
120 <remove value="&quot;"/>
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="&quot;"/>
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="&quot;"/>
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 -&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.)"/>
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>