Mercurial > repos > galaxyp > openms_isobaricanalyzer
comparison IsobaricAnalyzer.xml @ 13:130ffca1ec5b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:12:40 +0000 |
parents | 57a06b90bb00 |
children | 30f67afbf5be |
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12:e306864ec5b1 | 13:130ffca1ec5b |
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1 <?xml version='1.0' encoding='UTF-8'?> | 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 CTDConverter.--> | 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
3 <!--Proposed Tool Section: [Quantitation]--> | 3 <!--Proposed Tool Section: [Quantitation]--> |
4 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Calculates isobaric quantitative values for peptides</description> | 5 <description>Calculates isobaric quantitative values for peptides</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">IsobaricAnalyzer</token> | 7 <token name="@EXECUTABLE@">IsobaricAnalyzer</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
11 </macros> | 9 </macros> |
12 <expand macro="requirements"/> | 10 <expand macro="requirements"/> |
13 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
15 @EXT_FOO@ | 13 @EXT_FOO@ |
39 <configfiles> | 37 <configfiles> |
40 <inputs name="args_json" data_style="paths"/> | 38 <inputs name="args_json" data_style="paths"/> |
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
42 </configfiles> | 40 </configfiles> |
43 <inputs> | 41 <inputs> |
44 <param name="type" argument="-type" type="select" optional="false" label="Isobaric Quantitation method used in the experiment" help=""> | 42 <param argument="-type" type="select" optional="true" label="Isobaric Quantitation method used in the experiment" help=""> |
45 <option value="itraq4plex" selected="true">itraq4plex</option> | 43 <option value="itraq4plex" selected="true">itraq4plex</option> |
46 <option value="itraq8plex">itraq8plex</option> | 44 <option value="itraq8plex">itraq8plex</option> |
47 <option value="tmt10plex">tmt10plex</option> | 45 <option value="tmt10plex">tmt10plex</option> |
48 <option value="tmt11plex">tmt11plex</option> | 46 <option value="tmt11plex">tmt11plex</option> |
49 <option value="tmt16plex">tmt16plex</option> | 47 <option value="tmt16plex">tmt16plex</option> |
50 <option value="tmt6plex">tmt6plex</option> | 48 <option value="tmt6plex">tmt6plex</option> |
51 <expand macro="list_string_san"/> | 49 <expand macro="list_string_san" name="type"/> |
52 </param> | 50 </param> |
53 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input raw/picked data file" help=" select mzml data sets(s)"/> | 51 <param argument="-in" type="data" format="mzml" optional="false" label="input raw/picked data file" help=" select mzml data sets(s)"/> |
54 <section name="extraction" title="Parameters for the channel extraction" help="" expanded="false"> | 52 <section name="extraction" title="Parameters for the channel extraction" help="" expanded="false"> |
55 <param name="select_activation" argument="-extraction:select_activation" type="select" optional="false" label="Operate only on MSn scans where any of its precursors features a certain activation method" help="(e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering"> | 53 <param name="select_activation" argument="-extraction:select_activation" type="select" optional="true" label="Operate only on MSn scans where any of its precursors features a certain activation method" help="Setting to "auto" uses HCD and HCID spectra. Set to empty string if you want to disable filtering"> |
54 <option value="auto" selected="true">auto</option> | |
56 <option value="Collision-induced dissociation">Collision-induced dissociation</option> | 55 <option value="Collision-induced dissociation">Collision-induced dissociation</option> |
57 <option value="Post-source decay">Post-source decay</option> | 56 <option value="Post-source decay">Post-source decay</option> |
58 <option value="Plasma desorption">Plasma desorption</option> | 57 <option value="Plasma desorption">Plasma desorption</option> |
59 <option value="Surface-induced dissociation">Surface-induced dissociation</option> | 58 <option value="Surface-induced dissociation">Surface-induced dissociation</option> |
60 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> | 59 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> |
61 <option value="Electron capture dissociation">Electron capture dissociation</option> | 60 <option value="Electron capture dissociation">Electron capture dissociation</option> |
62 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> | 61 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> |
63 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> | 62 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> |
64 <option value="High-energy collision-induced dissociation" selected="true">High-energy collision-induced dissociation</option> | 63 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> |
65 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> | 64 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> |
66 <option value="Photodissociation">Photodissociation</option> | 65 <option value="Photodissociation">Photodissociation</option> |
67 <option value="Electron transfer dissociation">Electron transfer dissociation</option> | 66 <option value="Electron transfer dissociation">Electron transfer dissociation</option> |
67 <option value="Pulsed q dissociation">Pulsed q dissociation</option> | |
68 <option value="trap-type collision-induced dissociation">trap-type collision-induced dissociation</option> | |
69 <option value="beam-type collision-induced dissociation">beam-type collision-induced dissociation</option> | |
70 <option value="in-source collision-induced dissociation">in-source collision-induced dissociation</option> | |
68 <option value=""></option> | 71 <option value=""></option> |
69 <expand macro="list_string_san"/> | 72 <expand macro="list_string_san" name="select_activation"/> |
70 </param> | 73 </param> |
71 <param name="reporter_mass_shift" argument="-extraction:reporter_mass_shift" type="float" optional="true" min="0.0001" max="0.5" value="0.002" label="Allowed shift (left to right) in Th from the expected position" help=""/> | 74 <param name="reporter_mass_shift" argument="-extraction:reporter_mass_shift" type="float" optional="true" min="0.0001" max="0.5" value="0.002" label="Allowed shift (left to right) in Th from the expected position" help=""/> |
72 <param name="min_precursor_intensity" argument="-extraction:min_precursor_intensity" type="float" optional="true" min="0.0" value="1.0" label="Minimum intensity of the precursor to be extracted" help="MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/> | 75 <param name="min_precursor_intensity" argument="-extraction:min_precursor_intensity" type="float" optional="true" min="0.0" value="1.0" label="Minimum intensity of the precursor to be extracted" help="MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/> |
73 <param name="keep_unannotated_precursor" argument="-extraction:keep_unannotated_precursor" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help=""/> | 76 <param name="keep_unannotated_precursor" argument="-extraction:keep_unannotated_precursor" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help=""/> |
74 <param name="min_reporter_intensity" argument="-extraction:min_reporter_intensity" type="float" optional="true" min="0.0" value="0.0" label="Minimum intensity of the individual reporter ions to be extracted" help=""/> | 77 <param name="min_reporter_intensity" argument="-extraction:min_reporter_intensity" type="float" optional="true" min="0.0" value="0.0" label="Minimum intensity of the individual reporter ions to be extracted" help=""/> |
77 <param name="precursor_isotope_deviation" argument="-extraction:precursor_isotope_deviation" type="float" optional="true" min="0.0" value="10.0" label="Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precurso" help=""/> | 80 <param name="precursor_isotope_deviation" argument="-extraction:precursor_isotope_deviation" type="float" optional="true" min="0.0" value="10.0" label="Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precurso" help=""/> |
78 <param name="purity_interpolation" argument="-extraction:purity_interpolation" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If set to true the algorithm will try to compute the purity as a time weighted linear combination of the precursor scan and the following scan" help="If set to false, only the precursor scan will be used"/> | 81 <param name="purity_interpolation" argument="-extraction:purity_interpolation" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If set to true the algorithm will try to compute the purity as a time weighted linear combination of the precursor scan and the following scan" help="If set to false, only the precursor scan will be used"/> |
79 </section> | 82 </section> |
80 <section name="itraq4plex" title="Algorithm parameters for iTRAQ 4-plex" help="" expanded="false"> | 83 <section name="itraq4plex" title="Algorithm parameters for iTRAQ 4-plex" help="" expanded="false"> |
81 <param name="channel_114_description" argument="-itraq4plex:channel_114_description" type="text" optional="true" value="" label="Description for the content of the 114 channel" help=""> | 84 <param name="channel_114_description" argument="-itraq4plex:channel_114_description" type="text" optional="true" value="" label="Description for the content of the 114 channel" help=""> |
82 <expand macro="list_string_san"/> | 85 <expand macro="list_string_san" name="channel_114_description"/> |
83 </param> | 86 </param> |
84 <param name="channel_115_description" argument="-itraq4plex:channel_115_description" type="text" optional="true" value="" label="Description for the content of the 115 channel" help=""> | 87 <param name="channel_115_description" argument="-itraq4plex:channel_115_description" type="text" optional="true" value="" label="Description for the content of the 115 channel" help=""> |
85 <expand macro="list_string_san"/> | 88 <expand macro="list_string_san" name="channel_115_description"/> |
86 </param> | 89 </param> |
87 <param name="channel_116_description" argument="-itraq4plex:channel_116_description" type="text" optional="true" value="" label="Description for the content of the 116 channel" help=""> | 90 <param name="channel_116_description" argument="-itraq4plex:channel_116_description" type="text" optional="true" value="" label="Description for the content of the 116 channel" help=""> |
88 <expand macro="list_string_san"/> | 91 <expand macro="list_string_san" name="channel_116_description"/> |
89 </param> | 92 </param> |
90 <param name="channel_117_description" argument="-itraq4plex:channel_117_description" type="text" optional="true" value="" label="Description for the content of the 117 channel" help=""> | 93 <param name="channel_117_description" argument="-itraq4plex:channel_117_description" type="text" optional="true" value="" label="Description for the content of the 117 channel" help=""> |
91 <expand macro="list_string_san"/> | 94 <expand macro="list_string_san" name="channel_117_description"/> |
92 </param> | 95 </param> |
93 <param name="reference_channel" argument="-itraq4plex:reference_channel" type="integer" optional="true" min="114" max="117" value="114" label="Number of the reference channel (114-117)" help=""/> | 96 <param name="reference_channel" argument="-itraq4plex:reference_channel" type="integer" optional="true" min="114" max="117" value="114" label="Number of the reference channel (114-117)" help=""/> |
94 <param name="correction_matrix" argument="-itraq4plex:correction_matrix" type="text" optional="true" value="0.0/1.0/5.9/0.2 0.0/2.0/5.6/0.1 0.0/3.0/4.5/0.1 0.1/4.0/3.5/0.1" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> | 97 <param name="correction_matrix" argument="-itraq4plex:correction_matrix" type="text" optional="true" value="0.0/1.0/5.9/0.2 0.0/2.0/5.6/0.1 0.0/3.0/4.5/0.1 0.1/4.0/3.5/0.1" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
95 <expand macro="list_string_val"/> | 98 <expand macro="list_string_val" name="correction_matrix"/> |
96 <expand macro="list_string_san"/> | 99 <expand macro="list_string_san" name="correction_matrix"/> |
97 </param> | 100 </param> |
98 </section> | 101 </section> |
99 <section name="itraq8plex" title="Algorithm parameters for iTRAQ 8-plex" help="" expanded="false"> | 102 <section name="itraq8plex" title="Algorithm parameters for iTRAQ 8-plex" help="" expanded="false"> |
100 <param name="channel_113_description" argument="-itraq8plex:channel_113_description" type="text" optional="true" value="" label="Description for the content of the 113 channel" help=""> | 103 <param name="channel_113_description" argument="-itraq8plex:channel_113_description" type="text" optional="true" value="" label="Description for the content of the 113 channel" help=""> |
101 <expand macro="list_string_san"/> | 104 <expand macro="list_string_san" name="channel_113_description"/> |
102 </param> | 105 </param> |
103 <param name="channel_114_description" argument="-itraq8plex:channel_114_description" type="text" optional="true" value="" label="Description for the content of the 114 channel" help=""> | 106 <param name="channel_114_description" argument="-itraq8plex:channel_114_description" type="text" optional="true" value="" label="Description for the content of the 114 channel" help=""> |
104 <expand macro="list_string_san"/> | 107 <expand macro="list_string_san" name="channel_114_description"/> |
105 </param> | 108 </param> |
106 <param name="channel_115_description" argument="-itraq8plex:channel_115_description" type="text" optional="true" value="" label="Description for the content of the 115 channel" help=""> | 109 <param name="channel_115_description" argument="-itraq8plex:channel_115_description" type="text" optional="true" value="" label="Description for the content of the 115 channel" help=""> |
107 <expand macro="list_string_san"/> | 110 <expand macro="list_string_san" name="channel_115_description"/> |
108 </param> | 111 </param> |
109 <param name="channel_116_description" argument="-itraq8plex:channel_116_description" type="text" optional="true" value="" label="Description for the content of the 116 channel" help=""> | 112 <param name="channel_116_description" argument="-itraq8plex:channel_116_description" type="text" optional="true" value="" label="Description for the content of the 116 channel" help=""> |
110 <expand macro="list_string_san"/> | 113 <expand macro="list_string_san" name="channel_116_description"/> |
111 </param> | 114 </param> |
112 <param name="channel_117_description" argument="-itraq8plex:channel_117_description" type="text" optional="true" value="" label="Description for the content of the 117 channel" help=""> | 115 <param name="channel_117_description" argument="-itraq8plex:channel_117_description" type="text" optional="true" value="" label="Description for the content of the 117 channel" help=""> |
113 <expand macro="list_string_san"/> | 116 <expand macro="list_string_san" name="channel_117_description"/> |
114 </param> | 117 </param> |
115 <param name="channel_118_description" argument="-itraq8plex:channel_118_description" type="text" optional="true" value="" label="Description for the content of the 118 channel" help=""> | 118 <param name="channel_118_description" argument="-itraq8plex:channel_118_description" type="text" optional="true" value="" label="Description for the content of the 118 channel" help=""> |
116 <expand macro="list_string_san"/> | 119 <expand macro="list_string_san" name="channel_118_description"/> |
117 </param> | 120 </param> |
118 <param name="channel_119_description" argument="-itraq8plex:channel_119_description" type="text" optional="true" value="" label="Description for the content of the 119 channel" help=""> | 121 <param name="channel_119_description" argument="-itraq8plex:channel_119_description" type="text" optional="true" value="" label="Description for the content of the 119 channel" help=""> |
119 <expand macro="list_string_san"/> | 122 <expand macro="list_string_san" name="channel_119_description"/> |
120 </param> | 123 </param> |
121 <param name="channel_121_description" argument="-itraq8plex:channel_121_description" type="text" optional="true" value="" label="Description for the content of the 121 channel" help=""> | 124 <param name="channel_121_description" argument="-itraq8plex:channel_121_description" type="text" optional="true" value="" label="Description for the content of the 121 channel" help=""> |
122 <expand macro="list_string_san"/> | 125 <expand macro="list_string_san" name="channel_121_description"/> |
123 </param> | 126 </param> |
124 <param name="reference_channel" argument="-itraq8plex:reference_channel" type="integer" optional="true" min="113" max="121" value="113" label="Number of the reference channel (113-121)" help="Please note that 120 is not valid"/> | 127 <param name="reference_channel" argument="-itraq8plex:reference_channel" type="integer" optional="true" min="113" max="121" value="113" label="Number of the reference channel (113-121)" help="Please note that 120 is not valid"/> |
125 <param name="correction_matrix" argument="-itraq8plex:correction_matrix" type="text" optional="true" value="0.00/0.00/6.89/0.22 0.00/0.94/5.90/0.16 0.00/1.88/4.90/0.10 0.00/2.82/3.90/0.07 0.06/3.77/2.99/0.00 0.09/4.71/1.88/0.00 0.14/5.66/0.87/0.00 0.27/7.44/0.18/0.00" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> | 128 <param name="correction_matrix" argument="-itraq8plex:correction_matrix" type="text" optional="true" value="0.00/0.00/6.89/0.22 0.00/0.94/5.90/0.16 0.00/1.88/4.90/0.10 0.00/2.82/3.90/0.07 0.06/3.77/2.99/0.00 0.09/4.71/1.88/0.00 0.14/5.66/0.87/0.00 0.27/7.44/0.18/0.00" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
126 <expand macro="list_string_val"/> | 129 <expand macro="list_string_val" name="correction_matrix"/> |
127 <expand macro="list_string_san"/> | 130 <expand macro="list_string_san" name="correction_matrix"/> |
128 </param> | 131 </param> |
129 </section> | 132 </section> |
130 <section name="quantification" title="Parameters for the peptide quantification" help="" expanded="false"> | 133 <section name="quantification" title="Parameters for the peptide quantification" help="" expanded="false"> |
131 <param name="isotope_correction" argument="-quantification:isotope_correction" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable isotope correction (highly recommended)" help="Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results"/> | 134 <param name="isotope_correction" argument="-quantification:isotope_correction" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable isotope correction (highly recommended)" help="Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results"/> |
132 <param name="normalization" argument="-quantification:normalization" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable normalization of channel intensities with respect to the reference channel" help="The normalization is done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!"/> | 135 <param name="normalization" argument="-quantification:normalization" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable normalization of channel intensities with respect to the reference channel" help="The normalization is done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!"/> |
133 </section> | 136 </section> |
134 <section name="tmt10plex" title="Algorithm parameters for TMT 10-plex" help="" expanded="false"> | 137 <section name="tmt10plex" title="Algorithm parameters for TMT 10-plex" help="" expanded="false"> |
135 <param name="channel_126_description" argument="-tmt10plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help=""> | 138 <param name="channel_126_description" argument="-tmt10plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help=""> |
136 <expand macro="list_string_san"/> | 139 <expand macro="list_string_san" name="channel_126_description"/> |
137 </param> | 140 </param> |
138 <param name="channel_127N_description" argument="-tmt10plex:channel_127N_description" type="text" optional="true" value="" label="Description for the content of the 127N channel" help=""> | 141 <param name="channel_127N_description" argument="-tmt10plex:channel_127N_description" type="text" optional="true" value="" label="Description for the content of the 127N channel" help=""> |
139 <expand macro="list_string_san"/> | 142 <expand macro="list_string_san" name="channel_127N_description"/> |
140 </param> | 143 </param> |
141 <param name="channel_127C_description" argument="-tmt10plex:channel_127C_description" type="text" optional="true" value="" label="Description for the content of the 127C channel" help=""> | 144 <param name="channel_127C_description" argument="-tmt10plex:channel_127C_description" type="text" optional="true" value="" label="Description for the content of the 127C channel" help=""> |
142 <expand macro="list_string_san"/> | 145 <expand macro="list_string_san" name="channel_127C_description"/> |
143 </param> | 146 </param> |
144 <param name="channel_128N_description" argument="-tmt10plex:channel_128N_description" type="text" optional="true" value="" label="Description for the content of the 128N channel" help=""> | 147 <param name="channel_128N_description" argument="-tmt10plex:channel_128N_description" type="text" optional="true" value="" label="Description for the content of the 128N channel" help=""> |
145 <expand macro="list_string_san"/> | 148 <expand macro="list_string_san" name="channel_128N_description"/> |
146 </param> | 149 </param> |
147 <param name="channel_128C_description" argument="-tmt10plex:channel_128C_description" type="text" optional="true" value="" label="Description for the content of the 128C channel" help=""> | 150 <param name="channel_128C_description" argument="-tmt10plex:channel_128C_description" type="text" optional="true" value="" label="Description for the content of the 128C channel" help=""> |
148 <expand macro="list_string_san"/> | 151 <expand macro="list_string_san" name="channel_128C_description"/> |
149 </param> | 152 </param> |
150 <param name="channel_129N_description" argument="-tmt10plex:channel_129N_description" type="text" optional="true" value="" label="Description for the content of the 129N channel" help=""> | 153 <param name="channel_129N_description" argument="-tmt10plex:channel_129N_description" type="text" optional="true" value="" label="Description for the content of the 129N channel" help=""> |
151 <expand macro="list_string_san"/> | 154 <expand macro="list_string_san" name="channel_129N_description"/> |
152 </param> | 155 </param> |
153 <param name="channel_129C_description" argument="-tmt10plex:channel_129C_description" type="text" optional="true" value="" label="Description for the content of the 129C channel" help=""> | 156 <param name="channel_129C_description" argument="-tmt10plex:channel_129C_description" type="text" optional="true" value="" label="Description for the content of the 129C channel" help=""> |
154 <expand macro="list_string_san"/> | 157 <expand macro="list_string_san" name="channel_129C_description"/> |
155 </param> | 158 </param> |
156 <param name="channel_130N_description" argument="-tmt10plex:channel_130N_description" type="text" optional="true" value="" label="Description for the content of the 130N channel" help=""> | 159 <param name="channel_130N_description" argument="-tmt10plex:channel_130N_description" type="text" optional="true" value="" label="Description for the content of the 130N channel" help=""> |
157 <expand macro="list_string_san"/> | 160 <expand macro="list_string_san" name="channel_130N_description"/> |
158 </param> | 161 </param> |
159 <param name="channel_130C_description" argument="-tmt10plex:channel_130C_description" type="text" optional="true" value="" label="Description for the content of the 130C channel" help=""> | 162 <param name="channel_130C_description" argument="-tmt10plex:channel_130C_description" type="text" optional="true" value="" label="Description for the content of the 130C channel" help=""> |
160 <expand macro="list_string_san"/> | 163 <expand macro="list_string_san" name="channel_130C_description"/> |
161 </param> | 164 </param> |
162 <param name="channel_131_description" argument="-tmt10plex:channel_131_description" type="text" optional="true" value="" label="Description for the content of the 131 channel" help=""> | 165 <param name="channel_131_description" argument="-tmt10plex:channel_131_description" type="text" optional="true" value="" label="Description for the content of the 131 channel" help=""> |
163 <expand macro="list_string_san"/> | 166 <expand macro="list_string_san" name="channel_131_description"/> |
164 </param> | 167 </param> |
165 <param name="reference_channel" argument="-tmt10plex:reference_channel" type="select" optional="false" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" help=""> | 168 <param name="reference_channel" argument="-tmt10plex:reference_channel" type="select" optional="true" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" help=""> |
166 <option value="126" selected="true">126</option> | 169 <option value="126" selected="true">126</option> |
167 <option value="127N">127N</option> | 170 <option value="127N">127N</option> |
168 <option value="127C">127C</option> | 171 <option value="127C">127C</option> |
169 <option value="128N">128N</option> | 172 <option value="128N">128N</option> |
170 <option value="128C">128C</option> | 173 <option value="128C">128C</option> |
171 <option value="129N">129N</option> | 174 <option value="129N">129N</option> |
172 <option value="129C">129C</option> | 175 <option value="129C">129C</option> |
173 <option value="130N">130N</option> | 176 <option value="130N">130N</option> |
174 <option value="130C">130C</option> | 177 <option value="130C">130C</option> |
175 <option value="131">131</option> | 178 <option value="131">131</option> |
176 <expand macro="list_string_san"/> | 179 <expand macro="list_string_san" name="reference_channel"/> |
177 </param> | 180 </param> |
178 <param name="correction_matrix" argument="-tmt10plex:correction_matrix" type="text" optional="true" value="0.0/0.0/5.09/0.0 0.0/0.25/5.27/0.0 0.0/0.37/5.36/0.15 0.0/0.65/4.17/0.1 0.08/0.49/3.06/0.0 0.01/0.71/3.07/0.0 0.0/1.32/2.62/0.0 0.02/1.28/2.75/2.53 0.03/2.08/2.23/0.0 0.08/1.99/1.65/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> | 181 <param name="correction_matrix" argument="-tmt10plex:correction_matrix" type="text" optional="true" value="0.0/0.0/5.09/0.0 0.0/0.25/5.27/0.0 0.0/0.37/5.36/0.15 0.0/0.65/4.17/0.1 0.08/0.49/3.06/0.0 0.01/0.71/3.07/0.0 0.0/1.32/2.62/0.0 0.02/1.28/2.75/2.53 0.03/2.08/2.23/0.0 0.08/1.99/1.65/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
179 <expand macro="list_string_val"/> | 182 <expand macro="list_string_val" name="correction_matrix"/> |
180 <expand macro="list_string_san"/> | 183 <expand macro="list_string_san" name="correction_matrix"/> |
181 </param> | 184 </param> |
182 </section> | 185 </section> |
183 <section name="tmt11plex" title="Algorithm parameters for TMT 11-plex" help="" expanded="false"> | 186 <section name="tmt11plex" title="Algorithm parameters for TMT 11-plex" help="" expanded="false"> |
184 <param name="channel_126_description" argument="-tmt11plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help=""> | 187 <param name="channel_126_description" argument="-tmt11plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help=""> |
185 <expand macro="list_string_san"/> | 188 <expand macro="list_string_san" name="channel_126_description"/> |
186 </param> | 189 </param> |
187 <param name="channel_127N_description" argument="-tmt11plex:channel_127N_description" type="text" optional="true" value="" label="Description for the content of the 127N channel" help=""> | 190 <param name="channel_127N_description" argument="-tmt11plex:channel_127N_description" type="text" optional="true" value="" label="Description for the content of the 127N channel" help=""> |
188 <expand macro="list_string_san"/> | 191 <expand macro="list_string_san" name="channel_127N_description"/> |
189 </param> | 192 </param> |
190 <param name="channel_127C_description" argument="-tmt11plex:channel_127C_description" type="text" optional="true" value="" label="Description for the content of the 127C channel" help=""> | 193 <param name="channel_127C_description" argument="-tmt11plex:channel_127C_description" type="text" optional="true" value="" label="Description for the content of the 127C channel" help=""> |
191 <expand macro="list_string_san"/> | 194 <expand macro="list_string_san" name="channel_127C_description"/> |
192 </param> | 195 </param> |
193 <param name="channel_128N_description" argument="-tmt11plex:channel_128N_description" type="text" optional="true" value="" label="Description for the content of the 128N channel" help=""> | 196 <param name="channel_128N_description" argument="-tmt11plex:channel_128N_description" type="text" optional="true" value="" label="Description for the content of the 128N channel" help=""> |
194 <expand macro="list_string_san"/> | 197 <expand macro="list_string_san" name="channel_128N_description"/> |
195 </param> | 198 </param> |
196 <param name="channel_128C_description" argument="-tmt11plex:channel_128C_description" type="text" optional="true" value="" label="Description for the content of the 128C channel" help=""> | 199 <param name="channel_128C_description" argument="-tmt11plex:channel_128C_description" type="text" optional="true" value="" label="Description for the content of the 128C channel" help=""> |
197 <expand macro="list_string_san"/> | 200 <expand macro="list_string_san" name="channel_128C_description"/> |
198 </param> | 201 </param> |
199 <param name="channel_129N_description" argument="-tmt11plex:channel_129N_description" type="text" optional="true" value="" label="Description for the content of the 129N channel" help=""> | 202 <param name="channel_129N_description" argument="-tmt11plex:channel_129N_description" type="text" optional="true" value="" label="Description for the content of the 129N channel" help=""> |
200 <expand macro="list_string_san"/> | 203 <expand macro="list_string_san" name="channel_129N_description"/> |
201 </param> | 204 </param> |
202 <param name="channel_129C_description" argument="-tmt11plex:channel_129C_description" type="text" optional="true" value="" label="Description for the content of the 129C channel" help=""> | 205 <param name="channel_129C_description" argument="-tmt11plex:channel_129C_description" type="text" optional="true" value="" label="Description for the content of the 129C channel" help=""> |
203 <expand macro="list_string_san"/> | 206 <expand macro="list_string_san" name="channel_129C_description"/> |
204 </param> | 207 </param> |
205 <param name="channel_130N_description" argument="-tmt11plex:channel_130N_description" type="text" optional="true" value="" label="Description for the content of the 130N channel" help=""> | 208 <param name="channel_130N_description" argument="-tmt11plex:channel_130N_description" type="text" optional="true" value="" label="Description for the content of the 130N channel" help=""> |
206 <expand macro="list_string_san"/> | 209 <expand macro="list_string_san" name="channel_130N_description"/> |
207 </param> | 210 </param> |
208 <param name="channel_130C_description" argument="-tmt11plex:channel_130C_description" type="text" optional="true" value="" label="Description for the content of the 130C channel" help=""> | 211 <param name="channel_130C_description" argument="-tmt11plex:channel_130C_description" type="text" optional="true" value="" label="Description for the content of the 130C channel" help=""> |
209 <expand macro="list_string_san"/> | 212 <expand macro="list_string_san" name="channel_130C_description"/> |
210 </param> | 213 </param> |
211 <param name="channel_131N_description" argument="-tmt11plex:channel_131N_description" type="text" optional="true" value="" label="Description for the content of the 131N channel" help=""> | 214 <param name="channel_131N_description" argument="-tmt11plex:channel_131N_description" type="text" optional="true" value="" label="Description for the content of the 131N channel" help=""> |
212 <expand macro="list_string_san"/> | 215 <expand macro="list_string_san" name="channel_131N_description"/> |
213 </param> | 216 </param> |
214 <param name="channel_131C_description" argument="-tmt11plex:channel_131C_description" type="text" optional="true" value="" label="Description for the content of the 131C channel" help=""> | 217 <param name="channel_131C_description" argument="-tmt11plex:channel_131C_description" type="text" optional="true" value="" label="Description for the content of the 131C channel" help=""> |
215 <expand macro="list_string_san"/> | 218 <expand macro="list_string_san" name="channel_131C_description"/> |
216 </param> | 219 </param> |
217 <param name="reference_channel" argument="-tmt11plex:reference_channel" type="select" optional="false" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help=""> | 220 <param name="reference_channel" argument="-tmt11plex:reference_channel" type="select" optional="true" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help=""> |
218 <option value="126" selected="true">126</option> | 221 <option value="126" selected="true">126</option> |
219 <option value="127N">127N</option> | 222 <option value="127N">127N</option> |
220 <option value="127C">127C</option> | 223 <option value="127C">127C</option> |
221 <option value="128N">128N</option> | 224 <option value="128N">128N</option> |
222 <option value="128C">128C</option> | 225 <option value="128C">128C</option> |
224 <option value="129C">129C</option> | 227 <option value="129C">129C</option> |
225 <option value="130N">130N</option> | 228 <option value="130N">130N</option> |
226 <option value="130C">130C</option> | 229 <option value="130C">130C</option> |
227 <option value="131N">131N</option> | 230 <option value="131N">131N</option> |
228 <option value="131C">131C</option> | 231 <option value="131C">131C</option> |
229 <expand macro="list_string_san"/> | 232 <expand macro="list_string_san" name="reference_channel"/> |
230 </param> | 233 </param> |
231 <param name="correction_matrix" argument="-tmt11plex:correction_matrix" type="text" optional="true" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> | 234 <param name="correction_matrix" argument="-tmt11plex:correction_matrix" type="text" optional="true" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
232 <expand macro="list_string_val"/> | 235 <expand macro="list_string_val" name="correction_matrix"/> |
233 <expand macro="list_string_san"/> | 236 <expand macro="list_string_san" name="correction_matrix"/> |
234 </param> | 237 </param> |
235 </section> | 238 </section> |
236 <section name="tmt16plex" title="Algorithm parameters for TMT 16-plex" help="" expanded="false"> | 239 <section name="tmt16plex" title="Algorithm parameters for TMT 16-plex" help="" expanded="false"> |
237 <param name="channel_126_description" argument="-tmt16plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help=""> | 240 <param name="channel_126_description" argument="-tmt16plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help=""> |
238 <expand macro="list_string_san"/> | 241 <expand macro="list_string_san" name="channel_126_description"/> |
239 </param> | 242 </param> |
240 <param name="channel_127N_description" argument="-tmt16plex:channel_127N_description" type="text" optional="true" value="" label="Description for the content of the 127N channel" help=""> | 243 <param name="channel_127N_description" argument="-tmt16plex:channel_127N_description" type="text" optional="true" value="" label="Description for the content of the 127N channel" help=""> |
241 <expand macro="list_string_san"/> | 244 <expand macro="list_string_san" name="channel_127N_description"/> |
242 </param> | 245 </param> |
243 <param name="channel_127C_description" argument="-tmt16plex:channel_127C_description" type="text" optional="true" value="" label="Description for the content of the 127C channel" help=""> | 246 <param name="channel_127C_description" argument="-tmt16plex:channel_127C_description" type="text" optional="true" value="" label="Description for the content of the 127C channel" help=""> |
244 <expand macro="list_string_san"/> | 247 <expand macro="list_string_san" name="channel_127C_description"/> |
245 </param> | 248 </param> |
246 <param name="channel_128N_description" argument="-tmt16plex:channel_128N_description" type="text" optional="true" value="" label="Description for the content of the 128N channel" help=""> | 249 <param name="channel_128N_description" argument="-tmt16plex:channel_128N_description" type="text" optional="true" value="" label="Description for the content of the 128N channel" help=""> |
247 <expand macro="list_string_san"/> | 250 <expand macro="list_string_san" name="channel_128N_description"/> |
248 </param> | 251 </param> |
249 <param name="channel_128C_description" argument="-tmt16plex:channel_128C_description" type="text" optional="true" value="" label="Description for the content of the 128C channel" help=""> | 252 <param name="channel_128C_description" argument="-tmt16plex:channel_128C_description" type="text" optional="true" value="" label="Description for the content of the 128C channel" help=""> |
250 <expand macro="list_string_san"/> | 253 <expand macro="list_string_san" name="channel_128C_description"/> |
251 </param> | 254 </param> |
252 <param name="channel_129N_description" argument="-tmt16plex:channel_129N_description" type="text" optional="true" value="" label="Description for the content of the 129N channel" help=""> | 255 <param name="channel_129N_description" argument="-tmt16plex:channel_129N_description" type="text" optional="true" value="" label="Description for the content of the 129N channel" help=""> |
253 <expand macro="list_string_san"/> | 256 <expand macro="list_string_san" name="channel_129N_description"/> |
254 </param> | 257 </param> |
255 <param name="channel_129C_description" argument="-tmt16plex:channel_129C_description" type="text" optional="true" value="" label="Description for the content of the 129C channel" help=""> | 258 <param name="channel_129C_description" argument="-tmt16plex:channel_129C_description" type="text" optional="true" value="" label="Description for the content of the 129C channel" help=""> |
256 <expand macro="list_string_san"/> | 259 <expand macro="list_string_san" name="channel_129C_description"/> |
257 </param> | 260 </param> |
258 <param name="channel_130N_description" argument="-tmt16plex:channel_130N_description" type="text" optional="true" value="" label="Description for the content of the 130N channel" help=""> | 261 <param name="channel_130N_description" argument="-tmt16plex:channel_130N_description" type="text" optional="true" value="" label="Description for the content of the 130N channel" help=""> |
259 <expand macro="list_string_san"/> | 262 <expand macro="list_string_san" name="channel_130N_description"/> |
260 </param> | 263 </param> |
261 <param name="channel_130C_description" argument="-tmt16plex:channel_130C_description" type="text" optional="true" value="" label="Description for the content of the 130C channel" help=""> | 264 <param name="channel_130C_description" argument="-tmt16plex:channel_130C_description" type="text" optional="true" value="" label="Description for the content of the 130C channel" help=""> |
262 <expand macro="list_string_san"/> | 265 <expand macro="list_string_san" name="channel_130C_description"/> |
263 </param> | 266 </param> |
264 <param name="channel_131N_description" argument="-tmt16plex:channel_131N_description" type="text" optional="true" value="" label="Description for the content of the 131N channel" help=""> | 267 <param name="channel_131N_description" argument="-tmt16plex:channel_131N_description" type="text" optional="true" value="" label="Description for the content of the 131N channel" help=""> |
265 <expand macro="list_string_san"/> | 268 <expand macro="list_string_san" name="channel_131N_description"/> |
266 </param> | 269 </param> |
267 <param name="channel_131C_description" argument="-tmt16plex:channel_131C_description" type="text" optional="true" value="" label="Description for the content of the 131C channel" help=""> | 270 <param name="channel_131C_description" argument="-tmt16plex:channel_131C_description" type="text" optional="true" value="" label="Description for the content of the 131C channel" help=""> |
268 <expand macro="list_string_san"/> | 271 <expand macro="list_string_san" name="channel_131C_description"/> |
269 </param> | 272 </param> |
270 <param name="channel_132N_description" argument="-tmt16plex:channel_132N_description" type="text" optional="true" value="" label="Description for the content of the 132N channel" help=""> | 273 <param name="channel_132N_description" argument="-tmt16plex:channel_132N_description" type="text" optional="true" value="" label="Description for the content of the 132N channel" help=""> |
271 <expand macro="list_string_san"/> | 274 <expand macro="list_string_san" name="channel_132N_description"/> |
272 </param> | 275 </param> |
273 <param name="channel_132C_description" argument="-tmt16plex:channel_132C_description" type="text" optional="true" value="" label="Description for the content of the 132C channel" help=""> | 276 <param name="channel_132C_description" argument="-tmt16plex:channel_132C_description" type="text" optional="true" value="" label="Description for the content of the 132C channel" help=""> |
274 <expand macro="list_string_san"/> | 277 <expand macro="list_string_san" name="channel_132C_description"/> |
275 </param> | 278 </param> |
276 <param name="channel_133N_description" argument="-tmt16plex:channel_133N_description" type="text" optional="true" value="" label="Description for the content of the 133N channel" help=""> | 279 <param name="channel_133N_description" argument="-tmt16plex:channel_133N_description" type="text" optional="true" value="" label="Description for the content of the 133N channel" help=""> |
277 <expand macro="list_string_san"/> | 280 <expand macro="list_string_san" name="channel_133N_description"/> |
278 </param> | 281 </param> |
279 <param name="channel_133C_description" argument="-tmt16plex:channel_133C_description" type="text" optional="true" value="" label="Description for the content of the 133C channel" help=""> | 282 <param name="channel_133C_description" argument="-tmt16plex:channel_133C_description" type="text" optional="true" value="" label="Description for the content of the 133C channel" help=""> |
280 <expand macro="list_string_san"/> | 283 <expand macro="list_string_san" name="channel_133C_description"/> |
281 </param> | 284 </param> |
282 <param name="channel_134N_description" argument="-tmt16plex:channel_134N_description" type="text" optional="true" value="" label="Description for the content of the 134N channel" help=""> | 285 <param name="channel_134N_description" argument="-tmt16plex:channel_134N_description" type="text" optional="true" value="" label="Description for the content of the 134N channel" help=""> |
283 <expand macro="list_string_san"/> | 286 <expand macro="list_string_san" name="channel_134N_description"/> |
284 </param> | 287 </param> |
285 <param name="reference_channel" argument="-tmt16plex:reference_channel" type="select" optional="false" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help=""> | 288 <param name="reference_channel" argument="-tmt16plex:reference_channel" type="select" optional="true" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help=""> |
286 <option value="126" selected="true">126</option> | 289 <option value="126" selected="true">126</option> |
287 <option value="127N">127N</option> | 290 <option value="127N">127N</option> |
288 <option value="127C">127C</option> | 291 <option value="127C">127C</option> |
289 <option value="128N">128N</option> | 292 <option value="128N">128N</option> |
290 <option value="128C">128C</option> | 293 <option value="128C">128C</option> |
297 <option value="132N">132N</option> | 300 <option value="132N">132N</option> |
298 <option value="132C">132C</option> | 301 <option value="132C">132C</option> |
299 <option value="133N">133N</option> | 302 <option value="133N">133N</option> |
300 <option value="133C">133C</option> | 303 <option value="133C">133C</option> |
301 <option value="134N">134N</option> | 304 <option value="134N">134N</option> |
302 <expand macro="list_string_san"/> | 305 <expand macro="list_string_san" name="reference_channel"/> |
303 </param> | 306 </param> |
304 <param name="correction_matrix" argument="-tmt16plex:correction_matrix" type="text" optional="true" value="0.0/0.0/8.02/0.0 0.0/0.68/7.46/0.0 0.0/0.71/6.94/0.0 0.0/1.88/6.67/0.0 0.0/1.34/5.59/0.0 0.0/2.41/5.48/0.0 0.0/2.34/5.19/0.0 0.0/3.53/4.57/0.0 0.0/2.67/4.16/0.0 0.0/3.92/3.73/0.0 0.0/3.69/3.14/0.0 0.0/3.22/2.76/0.0 0.0/4.11/2.0/0.0 0.0/3.85/1.58/0.0 0.0/4.63/1.18/0.0 0.0/5.22/0.86/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> | 307 <param name="correction_matrix" argument="-tmt16plex:correction_matrix" type="text" optional="true" value="0.0/0.0/8.02/0.0 0.0/0.68/7.46/0.0 0.0/0.71/6.94/0.0 0.0/1.88/6.67/0.0 0.0/1.34/5.59/0.0 0.0/2.41/5.48/0.0 0.0/2.34/5.19/0.0 0.0/3.53/4.57/0.0 0.0/2.67/4.16/0.0 0.0/3.92/3.73/0.0 0.0/3.69/3.14/0.0 0.0/3.22/2.76/0.0 0.0/4.11/2.0/0.0 0.0/3.85/1.58/0.0 0.0/4.63/1.18/0.0 0.0/5.22/0.86/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
305 <expand macro="list_string_val"/> | 308 <expand macro="list_string_val" name="correction_matrix"/> |
306 <expand macro="list_string_san"/> | 309 <expand macro="list_string_san" name="correction_matrix"/> |
307 </param> | 310 </param> |
308 </section> | 311 </section> |
309 <section name="tmt6plex" title="Algorithm parameters for TMT 6-plex" help="" expanded="false"> | 312 <section name="tmt6plex" title="Algorithm parameters for TMT 6-plex" help="" expanded="false"> |
310 <param name="channel_126_description" argument="-tmt6plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help=""> | 313 <param name="channel_126_description" argument="-tmt6plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help=""> |
311 <expand macro="list_string_san"/> | 314 <expand macro="list_string_san" name="channel_126_description"/> |
312 </param> | 315 </param> |
313 <param name="channel_127_description" argument="-tmt6plex:channel_127_description" type="text" optional="true" value="" label="Description for the content of the 127 channel" help=""> | 316 <param name="channel_127_description" argument="-tmt6plex:channel_127_description" type="text" optional="true" value="" label="Description for the content of the 127 channel" help=""> |
314 <expand macro="list_string_san"/> | 317 <expand macro="list_string_san" name="channel_127_description"/> |
315 </param> | 318 </param> |
316 <param name="channel_128_description" argument="-tmt6plex:channel_128_description" type="text" optional="true" value="" label="Description for the content of the 128 channel" help=""> | 319 <param name="channel_128_description" argument="-tmt6plex:channel_128_description" type="text" optional="true" value="" label="Description for the content of the 128 channel" help=""> |
317 <expand macro="list_string_san"/> | 320 <expand macro="list_string_san" name="channel_128_description"/> |
318 </param> | 321 </param> |
319 <param name="channel_129_description" argument="-tmt6plex:channel_129_description" type="text" optional="true" value="" label="Description for the content of the 129 channel" help=""> | 322 <param name="channel_129_description" argument="-tmt6plex:channel_129_description" type="text" optional="true" value="" label="Description for the content of the 129 channel" help=""> |
320 <expand macro="list_string_san"/> | 323 <expand macro="list_string_san" name="channel_129_description"/> |
321 </param> | 324 </param> |
322 <param name="channel_130_description" argument="-tmt6plex:channel_130_description" type="text" optional="true" value="" label="Description for the content of the 130 channel" help=""> | 325 <param name="channel_130_description" argument="-tmt6plex:channel_130_description" type="text" optional="true" value="" label="Description for the content of the 130 channel" help=""> |
323 <expand macro="list_string_san"/> | 326 <expand macro="list_string_san" name="channel_130_description"/> |
324 </param> | 327 </param> |
325 <param name="channel_131_description" argument="-tmt6plex:channel_131_description" type="text" optional="true" value="" label="Description for the content of the 131 channel" help=""> | 328 <param name="channel_131_description" argument="-tmt6plex:channel_131_description" type="text" optional="true" value="" label="Description for the content of the 131 channel" help=""> |
326 <expand macro="list_string_san"/> | 329 <expand macro="list_string_san" name="channel_131_description"/> |
327 </param> | 330 </param> |
328 <param name="reference_channel" argument="-tmt6plex:reference_channel" type="integer" optional="true" min="126" max="131" value="126" label="Number of the reference channel (126-131)" help=""/> | 331 <param name="reference_channel" argument="-tmt6plex:reference_channel" type="integer" optional="true" min="126" max="131" value="126" label="Number of the reference channel (126-131)" help=""/> |
329 <param name="correction_matrix" argument="-tmt6plex:correction_matrix" type="text" optional="true" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> | 332 <param name="correction_matrix" argument="-tmt6plex:correction_matrix" type="text" optional="true" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
330 <expand macro="list_string_val"/> | 333 <expand macro="list_string_val" name="correction_matrix"/> |
331 <expand macro="list_string_san"/> | 334 <expand macro="list_string_san" name="correction_matrix"/> |
332 </param> | 335 </param> |
333 </section> | 336 </section> |
334 <expand macro="adv_opts_macro"> | 337 <expand macro="adv_opts_macro"> |
335 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 338 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
336 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 339 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
337 <expand macro="list_string_san"/> | 340 <expand macro="list_string_san" name="test"/> |
338 </param> | 341 </param> |
339 </expand> | 342 </expand> |
340 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 343 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
341 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 344 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
342 </param> | 345 </param> |
345 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> | 348 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> |
346 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 349 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
347 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 350 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
348 </data> | 351 </data> |
349 </outputs> | 352 </outputs> |
350 <tests> | 353 <tests><!-- TOPP_IsobaricAnalyzer_1 --> |
351 <expand macro="autotest_IsobaricAnalyzer"/> | 354 <test expect_num_outputs="2"> |
352 <expand macro="manutest_IsobaricAnalyzer"/> | 355 <section name="adv_opts"> |
356 <param name="force" value="false"/> | |
357 <param name="test" value="true"/> | |
358 </section> | |
359 <param name="type" value="itraq4plex"/> | |
360 <param name="in" value="IsobaricAnalyzer_input_1.mzML"/> | |
361 <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> | |
362 <section name="extraction"> | |
363 <param name="select_activation"/> | |
364 <param name="reporter_mass_shift" value="0.1"/> | |
365 <param name="min_precursor_intensity" value="1.0"/> | |
366 <param name="keep_unannotated_precursor" value="true"/> | |
367 <param name="min_reporter_intensity" value="0.0"/> | |
368 <param name="discard_low_intensity_quantifications" value="false"/> | |
369 <param name="min_precursor_purity" value="0.0"/> | |
370 <param name="precursor_isotope_deviation" value="10.0"/> | |
371 <param name="purity_interpolation" value="true"/> | |
372 </section> | |
373 <section name="itraq4plex"> | |
374 <param name="channel_114_description" value="l1"/> | |
375 <param name="channel_115_description" value="l2"/> | |
376 <param name="channel_116_description" value="l3"/> | |
377 <param name="channel_117_description" value="lung"/> | |
378 <param name="reference_channel" value="114"/> | |
379 <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> | |
380 </section> | |
381 <section name="itraq8plex"> | |
382 <param name="channel_113_description" value=""/> | |
383 <param name="channel_114_description" value=""/> | |
384 <param name="channel_115_description" value=""/> | |
385 <param name="channel_116_description" value=""/> | |
386 <param name="channel_117_description" value=""/> | |
387 <param name="channel_118_description" value=""/> | |
388 <param name="channel_119_description" value=""/> | |
389 <param name="channel_121_description" value=""/> | |
390 <param name="reference_channel" value="113"/> | |
391 <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> | |
392 </section> | |
393 <section name="quantification"> | |
394 <param name="isotope_correction" value="true"/> | |
395 <param name="normalization" value="false"/> | |
396 </section> | |
397 <section name="tmt10plex"> | |
398 <param name="channel_126_description" value=""/> | |
399 <param name="channel_127N_description" value=""/> | |
400 <param name="channel_127C_description" value=""/> | |
401 <param name="channel_128N_description" value=""/> | |
402 <param name="channel_128C_description" value=""/> | |
403 <param name="channel_129N_description" value=""/> | |
404 <param name="channel_129C_description" value=""/> | |
405 <param name="channel_130N_description" value=""/> | |
406 <param name="channel_130C_description" value=""/> | |
407 <param name="channel_131_description" value=""/> | |
408 <param name="reference_channel" value="126"/> | |
409 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
410 </section> | |
411 <section name="tmt11plex"> | |
412 <param name="channel_126_description" value=""/> | |
413 <param name="channel_127N_description" value=""/> | |
414 <param name="channel_127C_description" value=""/> | |
415 <param name="channel_128N_description" value=""/> | |
416 <param name="channel_128C_description" value=""/> | |
417 <param name="channel_129N_description" value=""/> | |
418 <param name="channel_129C_description" value=""/> | |
419 <param name="channel_130N_description" value=""/> | |
420 <param name="channel_130C_description" value=""/> | |
421 <param name="channel_131N_description" value=""/> | |
422 <param name="channel_131C_description" value=""/> | |
423 <param name="reference_channel" value="126"/> | |
424 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
425 </section> | |
426 <section name="tmt16plex"> | |
427 <param name="channel_126_description" value=""/> | |
428 <param name="channel_127N_description" value=""/> | |
429 <param name="channel_127C_description" value=""/> | |
430 <param name="channel_128N_description" value=""/> | |
431 <param name="channel_128C_description" value=""/> | |
432 <param name="channel_129N_description" value=""/> | |
433 <param name="channel_129C_description" value=""/> | |
434 <param name="channel_130N_description" value=""/> | |
435 <param name="channel_130C_description" value=""/> | |
436 <param name="channel_131N_description" value=""/> | |
437 <param name="channel_131C_description" value=""/> | |
438 <param name="channel_132N_description" value=""/> | |
439 <param name="channel_132C_description" value=""/> | |
440 <param name="channel_133N_description" value=""/> | |
441 <param name="channel_133C_description" value=""/> | |
442 <param name="channel_134N_description" value=""/> | |
443 <param name="reference_channel" value="126"/> | |
444 <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> | |
445 </section> | |
446 <section name="tmt6plex"> | |
447 <param name="channel_126_description" value=""/> | |
448 <param name="channel_127_description" value=""/> | |
449 <param name="channel_128_description" value=""/> | |
450 <param name="channel_129_description" value=""/> | |
451 <param name="channel_130_description" value=""/> | |
452 <param name="channel_131_description" value=""/> | |
453 <param name="reference_channel" value="126"/> | |
454 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
455 </section> | |
456 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
457 <output name="ctd_out" ftype="xml"> | |
458 <assert_contents> | |
459 <is_valid_xml/> | |
460 </assert_contents> | |
461 </output> | |
462 </test> | |
463 <!-- TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1 --> | |
464 <test expect_num_outputs="2"> | |
465 <section name="adv_opts"> | |
466 <param name="force" value="false"/> | |
467 <param name="test" value="true"/> | |
468 </section> | |
469 <param name="type" value="itraq4plex"/> | |
470 <param name="in" value="TMTTenPlexMethod_test.mzML"/> | |
471 <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> | |
472 <section name="extraction"> | |
473 <param name="select_activation" value="auto"/> | |
474 <param name="reporter_mass_shift" value="0.002"/> | |
475 <param name="min_precursor_intensity" value="1.0"/> | |
476 <param name="keep_unannotated_precursor" value="true"/> | |
477 <param name="min_reporter_intensity" value="0.0"/> | |
478 <param name="discard_low_intensity_quantifications" value="false"/> | |
479 <param name="min_precursor_purity" value="0.0"/> | |
480 <param name="precursor_isotope_deviation" value="10.0"/> | |
481 <param name="purity_interpolation" value="true"/> | |
482 </section> | |
483 <section name="itraq4plex"> | |
484 <param name="channel_114_description" value=""/> | |
485 <param name="channel_115_description" value=""/> | |
486 <param name="channel_116_description" value=""/> | |
487 <param name="channel_117_description" value=""/> | |
488 <param name="reference_channel" value="114"/> | |
489 <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> | |
490 </section> | |
491 <section name="itraq8plex"> | |
492 <param name="channel_113_description" value=""/> | |
493 <param name="channel_114_description" value=""/> | |
494 <param name="channel_115_description" value=""/> | |
495 <param name="channel_116_description" value=""/> | |
496 <param name="channel_117_description" value=""/> | |
497 <param name="channel_118_description" value=""/> | |
498 <param name="channel_119_description" value=""/> | |
499 <param name="channel_121_description" value=""/> | |
500 <param name="reference_channel" value="113"/> | |
501 <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> | |
502 </section> | |
503 <section name="quantification"> | |
504 <param name="isotope_correction" value="true"/> | |
505 <param name="normalization" value="false"/> | |
506 </section> | |
507 <section name="tmt10plex"> | |
508 <param name="channel_126_description" value=""/> | |
509 <param name="channel_127N_description" value=""/> | |
510 <param name="channel_127C_description" value=""/> | |
511 <param name="channel_128N_description" value=""/> | |
512 <param name="channel_128C_description" value=""/> | |
513 <param name="channel_129N_description" value=""/> | |
514 <param name="channel_129C_description" value=""/> | |
515 <param name="channel_130N_description" value=""/> | |
516 <param name="channel_130C_description" value=""/> | |
517 <param name="channel_131_description" value=""/> | |
518 <param name="reference_channel" value="126"/> | |
519 <param name="correction_matrix" value=""0.0/0.0/5.0/0.0" "0.0/0.2/4.6/0.0" "0.0/0.2/4.6/0.3" "0.0/0.9/4.7/0.2" "0.0/0.5/3.2/0.0" "0.0/0.7/3.3/0.0" "0.0/1.3/2.5/0.0" "0.0/1.2/2.8/2.7" "0.0/1.5/2.0/0.0" "0.0/1.5/1.9/0.0""/> | |
520 </section> | |
521 <section name="tmt11plex"> | |
522 <param name="channel_126_description" value=""/> | |
523 <param name="channel_127N_description" value=""/> | |
524 <param name="channel_127C_description" value=""/> | |
525 <param name="channel_128N_description" value=""/> | |
526 <param name="channel_128C_description" value=""/> | |
527 <param name="channel_129N_description" value=""/> | |
528 <param name="channel_129C_description" value=""/> | |
529 <param name="channel_130N_description" value=""/> | |
530 <param name="channel_130C_description" value=""/> | |
531 <param name="channel_131N_description" value=""/> | |
532 <param name="channel_131C_description" value=""/> | |
533 <param name="reference_channel" value="126"/> | |
534 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
535 </section> | |
536 <section name="tmt16plex"> | |
537 <param name="channel_126_description" value=""/> | |
538 <param name="channel_127N_description" value=""/> | |
539 <param name="channel_127C_description" value=""/> | |
540 <param name="channel_128N_description" value=""/> | |
541 <param name="channel_128C_description" value=""/> | |
542 <param name="channel_129N_description" value=""/> | |
543 <param name="channel_129C_description" value=""/> | |
544 <param name="channel_130N_description" value=""/> | |
545 <param name="channel_130C_description" value=""/> | |
546 <param name="channel_131N_description" value=""/> | |
547 <param name="channel_131C_description" value=""/> | |
548 <param name="channel_132N_description" value=""/> | |
549 <param name="channel_132C_description" value=""/> | |
550 <param name="channel_133N_description" value=""/> | |
551 <param name="channel_133C_description" value=""/> | |
552 <param name="channel_134N_description" value=""/> | |
553 <param name="reference_channel" value="126"/> | |
554 <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> | |
555 </section> | |
556 <section name="tmt6plex"> | |
557 <param name="channel_126_description" value=""/> | |
558 <param name="channel_127_description" value=""/> | |
559 <param name="channel_128_description" value=""/> | |
560 <param name="channel_129_description" value=""/> | |
561 <param name="channel_130_description" value=""/> | |
562 <param name="channel_131_description" value=""/> | |
563 <param name="reference_channel" value="126"/> | |
564 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
565 </section> | |
566 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
567 <output name="ctd_out" ftype="xml"> | |
568 <assert_contents> | |
569 <is_valid_xml/> | |
570 </assert_contents> | |
571 </output> | |
572 </test> | |
573 <!-- TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1 --> | |
574 <test expect_num_outputs="2"> | |
575 <section name="adv_opts"> | |
576 <param name="force" value="false"/> | |
577 <param name="test" value="true"/> | |
578 </section> | |
579 <param name="type" value="itraq4plex"/> | |
580 <param name="in" value="TMTTenPlexMethod_test.mzML"/> | |
581 <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> | |
582 <section name="extraction"> | |
583 <param name="select_activation" value="auto"/> | |
584 <param name="reporter_mass_shift" value="0.002"/> | |
585 <param name="min_precursor_intensity" value="1.0"/> | |
586 <param name="keep_unannotated_precursor" value="true"/> | |
587 <param name="min_reporter_intensity" value="0.0"/> | |
588 <param name="discard_low_intensity_quantifications" value="false"/> | |
589 <param name="min_precursor_purity" value="0.0"/> | |
590 <param name="precursor_isotope_deviation" value="10.0"/> | |
591 <param name="purity_interpolation" value="true"/> | |
592 </section> | |
593 <section name="itraq4plex"> | |
594 <param name="channel_114_description" value=""/> | |
595 <param name="channel_115_description" value=""/> | |
596 <param name="channel_116_description" value=""/> | |
597 <param name="channel_117_description" value=""/> | |
598 <param name="reference_channel" value="114"/> | |
599 <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> | |
600 </section> | |
601 <section name="itraq8plex"> | |
602 <param name="channel_113_description" value=""/> | |
603 <param name="channel_114_description" value=""/> | |
604 <param name="channel_115_description" value=""/> | |
605 <param name="channel_116_description" value=""/> | |
606 <param name="channel_117_description" value=""/> | |
607 <param name="channel_118_description" value=""/> | |
608 <param name="channel_119_description" value=""/> | |
609 <param name="channel_121_description" value=""/> | |
610 <param name="reference_channel" value="113"/> | |
611 <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> | |
612 </section> | |
613 <section name="quantification"> | |
614 <param name="isotope_correction" value="true"/> | |
615 <param name="normalization" value="false"/> | |
616 </section> | |
617 <section name="tmt10plex"> | |
618 <param name="channel_126_description" value=""/> | |
619 <param name="channel_127N_description" value=""/> | |
620 <param name="channel_127C_description" value=""/> | |
621 <param name="channel_128N_description" value=""/> | |
622 <param name="channel_128C_description" value=""/> | |
623 <param name="channel_129N_description" value=""/> | |
624 <param name="channel_129C_description" value=""/> | |
625 <param name="channel_130N_description" value=""/> | |
626 <param name="channel_130C_description" value=""/> | |
627 <param name="channel_131_description" value=""/> | |
628 <param name="reference_channel" value="126"/> | |
629 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
630 </section> | |
631 <section name="tmt11plex"> | |
632 <param name="channel_126_description" value=""/> | |
633 <param name="channel_127N_description" value=""/> | |
634 <param name="channel_127C_description" value=""/> | |
635 <param name="channel_128N_description" value=""/> | |
636 <param name="channel_128C_description" value=""/> | |
637 <param name="channel_129N_description" value=""/> | |
638 <param name="channel_129C_description" value=""/> | |
639 <param name="channel_130N_description" value=""/> | |
640 <param name="channel_130C_description" value=""/> | |
641 <param name="channel_131N_description" value=""/> | |
642 <param name="channel_131C_description" value=""/> | |
643 <param name="reference_channel" value="126"/> | |
644 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
645 </section> | |
646 <section name="tmt16plex"> | |
647 <param name="channel_126_description" value=""/> | |
648 <param name="channel_127N_description" value=""/> | |
649 <param name="channel_127C_description" value=""/> | |
650 <param name="channel_128N_description" value=""/> | |
651 <param name="channel_128C_description" value=""/> | |
652 <param name="channel_129N_description" value=""/> | |
653 <param name="channel_129C_description" value=""/> | |
654 <param name="channel_130N_description" value=""/> | |
655 <param name="channel_130C_description" value=""/> | |
656 <param name="channel_131N_description" value=""/> | |
657 <param name="channel_131C_description" value=""/> | |
658 <param name="channel_132N_description" value=""/> | |
659 <param name="channel_132C_description" value=""/> | |
660 <param name="channel_133N_description" value=""/> | |
661 <param name="channel_133C_description" value=""/> | |
662 <param name="channel_134N_description" value=""/> | |
663 <param name="reference_channel" value="126"/> | |
664 <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> | |
665 </section> | |
666 <section name="tmt6plex"> | |
667 <param name="channel_126_description" value=""/> | |
668 <param name="channel_127_description" value=""/> | |
669 <param name="channel_128_description" value=""/> | |
670 <param name="channel_129_description" value=""/> | |
671 <param name="channel_130_description" value=""/> | |
672 <param name="channel_131_description" value=""/> | |
673 <param name="reference_channel" value="126"/> | |
674 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
675 </section> | |
676 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
677 <output name="ctd_out" ftype="xml"> | |
678 <assert_contents> | |
679 <is_valid_xml/> | |
680 </assert_contents> | |
681 </output> | |
682 </test> | |
683 <!-- TOPP_IsobaricAnalyzer_MS3TMT10Plex_1 --> | |
684 <test expect_num_outputs="2"> | |
685 <section name="adv_opts"> | |
686 <param name="force" value="false"/> | |
687 <param name="test" value="true"/> | |
688 </section> | |
689 <param name="type" value="tmt10plex"/> | |
690 <param name="in" value="MS3_nonHierarchical.mzML"/> | |
691 <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> | |
692 <section name="extraction"> | |
693 <param name="select_activation" value="Collision-induced dissociation"/> | |
694 <param name="reporter_mass_shift" value="0.002"/> | |
695 <param name="min_precursor_intensity" value="1.0"/> | |
696 <param name="keep_unannotated_precursor" value="true"/> | |
697 <param name="min_reporter_intensity" value="0.0"/> | |
698 <param name="discard_low_intensity_quantifications" value="false"/> | |
699 <param name="min_precursor_purity" value="0.0"/> | |
700 <param name="precursor_isotope_deviation" value="10.0"/> | |
701 <param name="purity_interpolation" value="true"/> | |
702 </section> | |
703 <section name="itraq4plex"> | |
704 <param name="channel_114_description" value=""/> | |
705 <param name="channel_115_description" value=""/> | |
706 <param name="channel_116_description" value=""/> | |
707 <param name="channel_117_description" value=""/> | |
708 <param name="reference_channel" value="114"/> | |
709 <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> | |
710 </section> | |
711 <section name="itraq8plex"> | |
712 <param name="channel_113_description" value=""/> | |
713 <param name="channel_114_description" value=""/> | |
714 <param name="channel_115_description" value=""/> | |
715 <param name="channel_116_description" value=""/> | |
716 <param name="channel_117_description" value=""/> | |
717 <param name="channel_118_description" value=""/> | |
718 <param name="channel_119_description" value=""/> | |
719 <param name="channel_121_description" value=""/> | |
720 <param name="reference_channel" value="113"/> | |
721 <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> | |
722 </section> | |
723 <section name="quantification"> | |
724 <param name="isotope_correction" value="true"/> | |
725 <param name="normalization" value="false"/> | |
726 </section> | |
727 <section name="tmt10plex"> | |
728 <param name="channel_126_description" value=""/> | |
729 <param name="channel_127N_description" value=""/> | |
730 <param name="channel_127C_description" value=""/> | |
731 <param name="channel_128N_description" value=""/> | |
732 <param name="channel_128C_description" value=""/> | |
733 <param name="channel_129N_description" value=""/> | |
734 <param name="channel_129C_description" value=""/> | |
735 <param name="channel_130N_description" value=""/> | |
736 <param name="channel_130C_description" value=""/> | |
737 <param name="channel_131_description" value=""/> | |
738 <param name="reference_channel" value="126"/> | |
739 <param name="correction_matrix" value=""0.0/0.0/5.09/0.0" "0.0/0.25/5.27/0.0" "0.0/0.37/5.36/0.15" "0.0/0.65/4.17/0.1" "0.08/0.49/3.06/0.0" "0.01/0.71/3.07/0.0" "0.0/1.32/2.62/0.0" "0.02/1.28/2.75/2.53" "0.03/2.08/2.23/0.0" "0.08/1.99/1.65/0.0""/> | |
740 </section> | |
741 <section name="tmt11plex"> | |
742 <param name="channel_126_description" value=""/> | |
743 <param name="channel_127N_description" value=""/> | |
744 <param name="channel_127C_description" value=""/> | |
745 <param name="channel_128N_description" value=""/> | |
746 <param name="channel_128C_description" value=""/> | |
747 <param name="channel_129N_description" value=""/> | |
748 <param name="channel_129C_description" value=""/> | |
749 <param name="channel_130N_description" value=""/> | |
750 <param name="channel_130C_description" value=""/> | |
751 <param name="channel_131N_description" value=""/> | |
752 <param name="channel_131C_description" value=""/> | |
753 <param name="reference_channel" value="126"/> | |
754 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
755 </section> | |
756 <section name="tmt16plex"> | |
757 <param name="channel_126_description" value=""/> | |
758 <param name="channel_127N_description" value=""/> | |
759 <param name="channel_127C_description" value=""/> | |
760 <param name="channel_128N_description" value=""/> | |
761 <param name="channel_128C_description" value=""/> | |
762 <param name="channel_129N_description" value=""/> | |
763 <param name="channel_129C_description" value=""/> | |
764 <param name="channel_130N_description" value=""/> | |
765 <param name="channel_130C_description" value=""/> | |
766 <param name="channel_131N_description" value=""/> | |
767 <param name="channel_131C_description" value=""/> | |
768 <param name="channel_132N_description" value=""/> | |
769 <param name="channel_132C_description" value=""/> | |
770 <param name="channel_133N_description" value=""/> | |
771 <param name="channel_133C_description" value=""/> | |
772 <param name="channel_134N_description" value=""/> | |
773 <param name="reference_channel" value="126"/> | |
774 <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> | |
775 </section> | |
776 <section name="tmt6plex"> | |
777 <param name="channel_126_description" value=""/> | |
778 <param name="channel_127_description" value=""/> | |
779 <param name="channel_128_description" value=""/> | |
780 <param name="channel_129_description" value=""/> | |
781 <param name="channel_130_description" value=""/> | |
782 <param name="channel_131_description" value=""/> | |
783 <param name="reference_channel" value="126"/> | |
784 <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> | |
785 </section> | |
786 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
787 <output name="ctd_out" ftype="xml"> | |
788 <assert_contents> | |
789 <is_valid_xml/> | |
790 </assert_contents> | |
791 </output> | |
792 </test> | |
353 </tests> | 793 </tests> |
354 <help><![CDATA[Calculates isobaric quantitative values for peptides | 794 <help><![CDATA[Calculates isobaric quantitative values for peptides |
355 | 795 |
356 | 796 |
357 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IsobaricAnalyzer.html]]></help> | 797 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IsobaricAnalyzer.html]]></help> |
358 <expand macro="references"/> | 798 <expand macro="references"/> |
359 </tool> | 799 </tool> |