Mercurial > repos > galaxyp > openms_isobaricanalyzer

comparison IsobaricAnalyzer.xml @ 13:130ffca1ec5b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:12:40 +0000
parents 57a06b90bb00
children 30f67afbf5be
comparison
equal deleted inserted replaced
12:e306864ec5b1 13:130ffca1ec5b
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 &quot;auto&quot; 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: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" 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: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" 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: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" 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: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" 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: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" 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: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" 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: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" 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: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" 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: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" 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: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" 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: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" 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: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" 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="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
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="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
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="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
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="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
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="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
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="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
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="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
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="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
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="&quot;0.0/0.0/5.0/0.0&quot; &quot;0.0/0.2/4.6/0.0&quot; &quot;0.0/0.2/4.6/0.3&quot; &quot;0.0/0.9/4.7/0.2&quot; &quot;0.0/0.5/3.2/0.0&quot; &quot;0.0/0.7/3.3/0.0&quot; &quot;0.0/1.3/2.5/0.0&quot; &quot;0.0/1.2/2.8/2.7&quot; &quot;0.0/1.5/2.0/0.0&quot; &quot;0.0/1.5/1.9/0.0&quot;"/>
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="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
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="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
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="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
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="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
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="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
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="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
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="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
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="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
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="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
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="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
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="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
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="&quot;0.0/0.0/5.09/0.0&quot; &quot;0.0/0.25/5.27/0.0&quot; &quot;0.0/0.37/5.36/0.15&quot; &quot;0.0/0.65/4.17/0.1&quot; &quot;0.08/0.49/3.06/0.0&quot; &quot;0.01/0.71/3.07/0.0&quot; &quot;0.0/1.32/2.62/0.0&quot; &quot;0.02/1.28/2.75/2.53&quot; &quot;0.03/2.08/2.23/0.0&quot; &quot;0.08/1.99/1.65/0.0&quot;"/>
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="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
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="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
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="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
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>