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comparison SpectraMerger.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="SpectraMerger" name="SpectraMerger" version="1.12.0"> 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 <description>Merges spectra (each MS level separately), increasing S/N ratios.</description> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <macros> 4 <tool id="SpectraMerger" name="SpectraMerger" version="2.0.0">
5 <token name="@EXECUTABLE@">SpectraMerger</token> 5 <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">SpectraMerger</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>SpectraMerger 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>SpectraMerger
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -merging_method ${param_merging_method} 17 #end if
15 -threads \${GALAXY_SLOTS:-24} 18 #if $param_out:
16 -algorithm:block_method:ms_levels ${param_ms_levels} 19 -out $param_out
17 -algorithm:block_method:rt_block_size ${param_rt_block_size} 20 #end if
18 -algorithm:block_method:rt_max_length ${param_rt_max_length} 21 #if $param_merging_method:
19 -algorithm:precursor_method:mz_tolerance ${param_mz_tolerance} 22 -merging_method
20 -algorithm:precursor_method:rt_tolerance ${param_rt_tolerance} 23 #if &quot; &quot; in str($param_merging_method):
24 &quot;$param_merging_method&quot;
25 #else
26 $param_merging_method
27 #end if
28 #end if
29 -threads \${GALAXY_SLOTS:-24}
30 #if $param_algorithm_average_gaussian_spectrum_type:
31 -algorithm:average_gaussian:spectrum_type
32 #if &quot; &quot; in str($param_algorithm_average_gaussian_spectrum_type):
33 &quot;$param_algorithm_average_gaussian_spectrum_type&quot;
34 #else
35 $param_algorithm_average_gaussian_spectrum_type
36 #end if
37 #end if
38 #if $param_algorithm_average_gaussian_ms_level:
39 -algorithm:average_gaussian:ms_level $param_algorithm_average_gaussian_ms_level
40 #end if
41 #if $param_algorithm_average_gaussian_rt_FWHM:
42 -algorithm:average_gaussian:rt_FWHM $param_algorithm_average_gaussian_rt_FWHM
43 #end if
44 #if $param_algorithm_average_tophat_spectrum_type:
45 -algorithm:average_tophat:spectrum_type
46 #if &quot; &quot; in str($param_algorithm_average_tophat_spectrum_type):
47 &quot;$param_algorithm_average_tophat_spectrum_type&quot;
48 #else
49 $param_algorithm_average_tophat_spectrum_type
50 #end if
51 #end if
52 #if $param_algorithm_average_tophat_ms_level:
53 -algorithm:average_tophat:ms_level $param_algorithm_average_tophat_ms_level
54 #end if
55 #if $param_algorithm_average_tophat_rt_range:
56 -algorithm:average_tophat:rt_range $param_algorithm_average_tophat_rt_range
57 #end if
58 #if $param_algorithm_average_tophat_rt_unit:
59 -algorithm:average_tophat:rt_unit
60 #if &quot; &quot; in str($param_algorithm_average_tophat_rt_unit):
61 &quot;$param_algorithm_average_tophat_rt_unit&quot;
62 #else
63 $param_algorithm_average_tophat_rt_unit
64 #end if
65 #end if
66
67 #if $rep_param_algorithm_block_method_ms_levels:
68 -algorithm:block_method:ms_levels
69 #for token in $rep_param_algorithm_block_method_ms_levels:
70 #if &quot; &quot; in str(token):
71 &quot;$token.param_algorithm_block_method_ms_levels&quot;
72 #else
73 $token.param_algorithm_block_method_ms_levels
74 #end if
75 #end for
76 #end if
77 #if $param_algorithm_block_method_rt_block_size:
78 -algorithm:block_method:rt_block_size $param_algorithm_block_method_rt_block_size
79 #end if
80 #if $param_algorithm_block_method_rt_max_length:
81 -algorithm:block_method:rt_max_length $param_algorithm_block_method_rt_max_length
82 #end if
83 #if $param_algorithm_precursor_method_mz_tolerance:
84 -algorithm:precursor_method:mz_tolerance $param_algorithm_precursor_method_mz_tolerance
85 #end if
86 #if $param_algorithm_precursor_method_rt_tolerance:
87 -algorithm:precursor_method:rt_tolerance $param_algorithm_precursor_method_rt_tolerance
88 #end if
21 #if $adv_opts.adv_opts_selector=='advanced': 89 #if $adv_opts.adv_opts_selector=='advanced':
22 -algorithm:mz_binning_width ${adv_opts.param_mz_binning_width} 90 #if $adv_opts.param_force:
23 -algorithm:mz_binning_width_unit ${adv_opts.param_mz_binning_width_unit} 91 -force
24 -algorithm:sort_blocks ${adv_opts.param_sort_blocks} 92 #end if
93 #if $adv_opts.param_algorithm_mz_binning_width:
94 -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width
95 #end if
96 #if $adv_opts.param_algorithm_mz_binning_width_unit:
97 -algorithm:mz_binning_width_unit
98 #if &quot; &quot; in str($adv_opts.param_algorithm_mz_binning_width_unit):
99 &quot;$adv_opts.param_algorithm_mz_binning_width_unit&quot;
100 #else
101 $adv_opts.param_algorithm_mz_binning_width_unit
102 #end if
103 #end if
104 #if $adv_opts.param_algorithm_sort_blocks:
105 -algorithm:sort_blocks
106 #if &quot; &quot; in str($adv_opts.param_algorithm_sort_blocks):
107 &quot;$adv_opts.param_algorithm_sort_blocks&quot;
108 #else
109 $adv_opts.param_algorithm_sort_blocks
110 #end if
111 #end if
112 #if $adv_opts.param_algorithm_average_gaussian_cutoff:
113 -algorithm:average_gaussian:cutoff $adv_opts.param_algorithm_average_gaussian_cutoff
114 #end if
25 #end if 115 #end if
26 </command> 116 </command>
27 <inputs> 117 <inputs>
28 <param name="param_in" type="data" format="mzML" optional="False" label="Input mzML file." help="(-in)"/> 118 <param format="mzml" help="(-in) " label="Input mzML file" name="param_in" optional="False" type="data"/>
29 <param name="param_merging_method" type="select" optional="True" value="block_method" label="Method of merging which should be used." help="(-merging_method)"> 119 <param help="(-merging_method) " label="Method of merging which should be used" name="param_merging_method" optional="True" type="select" value="average_gaussian">
30 <option value="precursor_method">precursor_method</option> 120 <option value="average_gaussian">average_gaussian</option>
31 <option value="block_method">block_method</option> 121 <option value="average_tophat">average_tophat</option>
32 </param> 122 <option value="precursor_method">precursor_method</option>
33 <param name="param_ms_levels" type="text" min="1" optional="True" size="20" value="1" label="Merge spectra of this level. All spectra with other MS levels remain untouched." help="(-ms_levels)"/> 123 <option value="block_method">block_method</option>
34 <param name="param_rt_block_size" type="integer" min="1" optional="True" value="5" label="Maximum number of scans to be summed up." help="(-rt_block_size)"/>
35 <param name="param_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)"/>
36 <param name="param_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)"/>
37 <param name="param_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)"/>
38 <expand macro="advanced_options">
39 <param name="param_mz_binning_width" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of two peaks to be merged." help="(-mz_binning_width)"/>
40 <param name="param_mz_binning_width_unit" type="select" optional="True" value="Da" label="Unit in which the distance between two peaks is given." help="(-mz_binning_width_unit)">
41 <option value="Da">Da</option>
42 <option value="ppm">ppm</option>
43 </param> 124 </param>
44 <param name="param_sort_blocks" type="select" optional="True" value="RT_ascending" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="(-sort_blocks)"> 125 <param help="(-spectrum_type) " label="Spectrum type of the MS level to be averaged" name="param_algorithm_average_gaussian_spectrum_type" optional="True" type="select" value="automatic">
45 <option value="RT_ascending">RT_ascending</option> 126 <option value="profile">profile</option>
46 <option value=" RT_descending"> RT_descending</option> 127 <option value="centroid">centroid</option>
128 <option value="automatic">automatic</option>
47 </param> 129 </param>
48 </expand> 130 <param help="(-ms_level) All other spectra remain unchanged" label="Average spectra of this level" min="1" name="param_algorithm_average_gaussian_ms_level" optional="True" type="integer" value="1"/>
49 </inputs> 131 <param help="(-rt_FWHM) " label="FWHM of Gauss curve in seconds to be averaged ove" max="1e+11" min="0.0" name="param_algorithm_average_gaussian_rt_FWHM" optional="True" type="float" value="5.0"/>
50 <outputs> 132 <param help="(-spectrum_type) " label="Spectrum type of the MS level to be averaged" name="param_algorithm_average_tophat_spectrum_type" optional="True" type="select" value="automatic">
51 <data name="param_out" label="Output mzML file with merged spectra." format="mzML"/> 133 <option value="profile">profile</option>
52 </outputs> 134 <option value="centroid">centroid</option>
53 <help>**What it does** 135 <option value="automatic">automatic</option>
54 136 </param>
55 Merges spectra (each MS level separately), increasing S/N ratios. 137 <param help="(-ms_level) All other spectra remain unchanged" label="Average spectra of this level" min="1" name="param_algorithm_average_tophat_ms_level" optional="True" type="integer" value="1"/>
138 <param help="(-rt_range) +/-(RT range)/2 from each spectrum" label="RT range to be averaged over, i.e" max="1e+11" min="0.0" name="param_algorithm_average_tophat_rt_range" optional="True" type="float" value="5.0"/>
139 <param help="(-rt_unit) " label="Unit for RT range" name="param_algorithm_average_tophat_rt_unit" optional="True" type="select" value="scans">
140 <option value="scans">scans</option>
141 <option value="seconds">seconds</option>
142 </param>
143 <repeat max="1" min="0" name="rep_param_algorithm_block_method_ms_levels" title="param_algorithm_block_method_ms_levels">
144 <param help="(-ms_levels) All spectra with other MS levels remain untouched" label="Merge spectra of this level" min="1" name="param_algorithm_block_method_ms_levels" optional="True" size="30" type="text" value="1">
145 <sanitizer>
146 <valid initial="string.printable">
147 <remove value="'"/>
148 <remove value="&quot;"/>
149 </valid>
150 </sanitizer>
151 </param>
152 </repeat>
153 <param help="(-rt_block_size) " label="Maximum number of scans to be summed up" min="1" name="param_algorithm_block_method_rt_block_size" optional="True" type="integer" value="5"/>
154 <param help="(-rt_max_length) " label="Maximum RT size of the block in seconds (0.0 = no size restriction)" max="1e+11" min="0.0" name="param_algorithm_block_method_rt_max_length" optional="True" type="float" value="0.0"/>
155 <param help="(-mz_tolerance) " label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" min="0.0" name="param_algorithm_precursor_method_mz_tolerance" optional="True" type="float" value="0.0001"/>
156 <param help="(-rt_tolerance) " label="Max RT distance of the precursor entries of two spectra to be merged in [s]" min="0.0" name="param_algorithm_precursor_method_rt_tolerance" optional="True" type="float" value="5.0"/>
157 <expand macro="advanced_options">
158 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
159 <param help="(-mz_binning_width) Closer data points or peaks will be merged" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" min="0.0" name="param_algorithm_mz_binning_width" optional="True" type="float" value="5.0"/>
160 <param help="(-mz_binning_width_unit) " label="Unit in which the distance between two data points or peaks is given" name="param_algorithm_mz_binning_width_unit" optional="True" type="select" value="ppm">
161 <option value="Da">Da</option>
162 <option value="ppm">ppm</option>
163 </param>
164 <param help="(-sort_blocks) " label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" name="param_algorithm_sort_blocks" optional="True" type="select" value="RT_ascending">
165 <option value="RT_ascending">RT_ascending</option>
166 <option value=" RT_descending"> RT_descending</option>
167 </param>
168 <param 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" label="Intensity cutoff for Gaussian" max="1.0" min="0.0" name="param_algorithm_average_gaussian_cutoff" optional="True" type="float" value="0.01"/>
169 </expand>
170 </inputs>
171 <outputs>
172 <data format="mzml" name="param_out"/>
173 </outputs>
174 <help>Merges spectra (each MS level separately), increasing S/N ratios.
56 175
57 176
58 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html 177 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html</help>
59 178 </tool>
60 @REFERENCES@
61 </help>
62 </tool>