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comparison SpectraMerger.xml @ 0:899812f5c032 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 12:42:48 -0500
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children 4a91d040aa01
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-1:000000000000 0:899812f5c032
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: [Signal processing and preprocessing]-->
4 <tool id="SpectraMerger" name="SpectraMerger" version="2.1.0">
5 <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
6 <macros>
7 <token name="@EXECUTABLE@">SpectraMerger</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>SpectraMerger
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_merging_method:
22 -merging_method $param_merging_method
23 #end if
24 #if $param_algorithm_average_gaussian_spectrum_type:
25 -algorithm:average_gaussian:spectrum_type $param_algorithm_average_gaussian_spectrum_type
26 #end if
27 #if $param_algorithm_average_gaussian_ms_level:
28 -algorithm:average_gaussian:ms_level $param_algorithm_average_gaussian_ms_level
29 #end if
30 #if $param_algorithm_average_gaussian_rt_FWHM:
31 -algorithm:average_gaussian:rt_FWHM $param_algorithm_average_gaussian_rt_FWHM
32 #end if
33 #if $param_algorithm_average_tophat_spectrum_type:
34 -algorithm:average_tophat:spectrum_type $param_algorithm_average_tophat_spectrum_type
35 #end if
36 #if $param_algorithm_average_tophat_ms_level:
37 -algorithm:average_tophat:ms_level $param_algorithm_average_tophat_ms_level
38 #end if
39 #if $param_algorithm_average_tophat_rt_range:
40 -algorithm:average_tophat:rt_range $param_algorithm_average_tophat_rt_range
41 #end if
42 #if $param_algorithm_average_tophat_rt_unit:
43 -algorithm:average_tophat:rt_unit $param_algorithm_average_tophat_rt_unit
44 #end if
45
46 #if $rep_param_algorithm_block_method_ms_levels:
47 -algorithm:block_method:ms_levels
48 #for token in $rep_param_algorithm_block_method_ms_levels:
49 #if " " in str(token):
50 "$token.param_algorithm_block_method_ms_levels"
51 #else
52 $token.param_algorithm_block_method_ms_levels
53 #end if
54 #end for
55 #end if
56 #if $param_algorithm_block_method_rt_block_size:
57 -algorithm:block_method:rt_block_size $param_algorithm_block_method_rt_block_size
58 #end if
59 #if $param_algorithm_block_method_rt_max_length:
60 -algorithm:block_method:rt_max_length $param_algorithm_block_method_rt_max_length
61 #end if
62 #if $param_algorithm_precursor_method_mz_tolerance:
63 -algorithm:precursor_method:mz_tolerance $param_algorithm_precursor_method_mz_tolerance
64 #end if
65 #if $param_algorithm_precursor_method_rt_tolerance:
66 -algorithm:precursor_method:rt_tolerance $param_algorithm_precursor_method_rt_tolerance
67 #end if
68 #if $adv_opts.adv_opts_selector=='advanced':
69 #if $adv_opts.param_force:
70 -force
71 #end if
72 #if $adv_opts.param_algorithm_mz_binning_width:
73 -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width
74 #end if
75 #if $adv_opts.param_algorithm_mz_binning_width_unit:
76 -algorithm:mz_binning_width_unit $adv_opts.param_algorithm_mz_binning_width_unit
77 #end if
78 #if $adv_opts.param_algorithm_sort_blocks:
79 -algorithm:sort_blocks $adv_opts.param_algorithm_sort_blocks
80 #end if
81 #if $adv_opts.param_algorithm_average_gaussian_cutoff:
82 -algorithm:average_gaussian:cutoff $adv_opts.param_algorithm_average_gaussian_cutoff
83 #end if
84 #end if
85 </command>
86 <inputs>
87 <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file" help="(-in) "/>
88 <param name="param_merging_method" display="radio" type="select" optional="False" value="average_gaussian" label="Method of merging which should be used" help="(-merging_method) ">
89 <option value="average_gaussian" selected="true">average_gaussian</option>
90 <option value="average_tophat">average_tophat</option>
91 <option value="precursor_method">precursor_method</option>
92 <option value="block_method">block_method</option>
93 </param>
94 <param name="param_algorithm_average_gaussian_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Spectrum type of the MS level to be averaged" help="(-spectrum_type) ">
95 <option value="profile">profile</option>
96 <option value="centroid">centroid</option>
97 <option value="automatic" selected="true">automatic</option>
98 </param>
99 <param name="param_algorithm_average_gaussian_ms_level" type="integer" min="1" optional="True" value="1" label="Average spectra of this level" help="(-ms_level) All other spectra remain unchanged"/>
100 <param name="param_algorithm_average_gaussian_rt_FWHM" type="float" min="0.0" max="1e+11" optional="True" value="5.0" label="FWHM of Gauss curve in seconds to be averaged ove" help="(-rt_FWHM) "/>
101 <param name="param_algorithm_average_tophat_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Spectrum type of the MS level to be averaged" help="(-spectrum_type) ">
102 <option value="profile">profile</option>
103 <option value="centroid">centroid</option>
104 <option value="automatic" selected="true">automatic</option>
105 </param>
106 <param name="param_algorithm_average_tophat_ms_level" type="integer" min="1" optional="True" value="1" label="Average spectra of this level" help="(-ms_level) All other spectra remain unchanged"/>
107 <param name="param_algorithm_average_tophat_rt_range" type="float" min="0.0" max="1e+11" optional="True" value="5.0" label="RT range to be averaged over, i.e" help="(-rt_range) +/-(RT range)/2 from each spectrum"/>
108 <param name="param_algorithm_average_tophat_rt_unit" display="radio" type="select" optional="False" value="scans" label="Unit for RT range" help="(-rt_unit) ">
109 <option value="scans" selected="true">scans</option>
110 <option value="seconds">seconds</option>
111 </param>
112 <repeat name="rep_param_algorithm_block_method_ms_levels" min="0" max="1" title="param_algorithm_block_method_ms_levels">
113 <param name="param_algorithm_block_method_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="Merge spectra of this level" help="(-ms_levels) All spectra with other MS levels remain untouched">
114 <sanitizer>
115 <valid initial="string.printable">
116 <remove value="'"/>
117 <remove value="&quot;"/>
118 </valid>
119 </sanitizer>
120 </param>
121 </repeat>
122 <param name="param_algorithm_block_method_rt_block_size" type="integer" min="1" optional="True" value="5" label="Maximum number of scans to be summed up" help="(-rt_block_size) "/>
123 <param name="param_algorithm_block_method_rt_max_length" type="float" min="0.0" max="1e+11" optional="True" value="0.0" label="Maximum RT size of the block in seconds (0.0 = no size restriction)" help="(-rt_max_length) "/>
124 <param name="param_algorithm_precursor_method_mz_tolerance" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help="(-mz_tolerance) "/>
125 <param name="param_algorithm_precursor_method_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]" help="(-rt_tolerance) "/>
126 <expand macro="advanced_options">
127 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
128 <param name="param_algorithm_mz_binning_width" type="float" min="0.0" optional="True" value="5.0" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" help="(-mz_binning_width) Closer data points or peaks will be merged"/>
129 <param name="param_algorithm_mz_binning_width_unit" display="radio" type="select" optional="False" value="ppm" label="Unit in which the distance between two data points or peaks is given" help="(-mz_binning_width_unit) ">
130 <option value="Da">Da</option>
131 <option value="ppm" selected="true">ppm</option>
132 </param>
133 <param name="param_algorithm_sort_blocks" display="radio" type="select" optional="False" value="RT_ascending" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="(-sort_blocks) ">
134 <option value="RT_ascending" selected="true">RT_ascending</option>
135 <option value=" RT_descending"> RT_descending</option>
136 </param>
137 <param name="param_algorithm_average_gaussian_cutoff" type="float" min="0.0" max="1.0" optional="True" value="0.01" label="Intensity cutoff for Gaussian" help="(-cutoff) The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average"/>
138 </expand>
139 </inputs>
140 <outputs>
141 <data name="param_out" format="mzml"/>
142 </outputs>
143 <help>Merges spectra (each MS level separately), increasing S/N ratios.
144
145
146 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html</help>
147 </tool>