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comparison IsobaricAnalyzer.xml @ 14:30f67afbf5be draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:32:32 +0000
parents 130ffca1ec5b
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13:130ffca1ec5b 14:30f67afbf5be
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Calculates isobaric quantitative values for peptides</description> 4 <description>Calculates isobaric quantitative values for peptides</description>
6 <macros> 5 <macros>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 19
21 ## Main program call 20 ## Main program call
22 21
23 set -o pipefail && 22 set -o pipefail &&
37 <configfiles> 36 <configfiles>
38 <inputs name="args_json" data_style="paths"/> 37 <inputs name="args_json" data_style="paths"/>
39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 </configfiles> 39 </configfiles>
41 <inputs> 40 <inputs>
42 <param argument="-type" type="select" optional="true" label="Isobaric Quantitation method used in the experiment" help=""> 41 <param argument="-type" type="select" label="Isobaric Quantitation method used in the experiment" help="">
43 <option value="itraq4plex" selected="true">itraq4plex</option> 42 <option value="itraq4plex" selected="true">itraq4plex</option>
44 <option value="itraq8plex">itraq8plex</option> 43 <option value="itraq8plex">itraq8plex</option>
45 <option value="tmt10plex">tmt10plex</option> 44 <option value="tmt10plex">tmt10plex</option>
46 <option value="tmt11plex">tmt11plex</option> 45 <option value="tmt11plex">tmt11plex</option>
47 <option value="tmt16plex">tmt16plex</option> 46 <option value="tmt16plex">tmt16plex</option>
47 <option value="tmt18plex">tmt18plex</option>
48 <option value="tmt6plex">tmt6plex</option> 48 <option value="tmt6plex">tmt6plex</option>
49 <expand macro="list_string_san" name="type"/> 49 <expand macro="list_string_san" name="type"/>
50 </param> 50 </param>
51 <param 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" label="input raw/picked data file" help=" select mzml data sets(s)"/>
52 <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">
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"> 53 <param name="select_activation" argument="-extraction:select_activation" type="select" 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> 54 <option value="auto" selected="true">auto</option>
55 <option value="Collision-induced dissociation">Collision-induced dissociation</option> 55 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
56 <option value="Post-source decay">Post-source decay</option> 56 <option value="Post-source decay">Post-source decay</option>
57 <option value="Plasma desorption">Plasma desorption</option> 57 <option value="Plasma desorption">Plasma desorption</option>
58 <option value="Surface-induced dissociation">Surface-induced dissociation</option> 58 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
66 <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> 67 <option value="Pulsed q dissociation">Pulsed q dissociation</option>
68 <option value="trap-type collision-induced dissociation">trap-type collision-induced 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> 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> 70 <option value="in-source collision-induced dissociation">in-source collision-induced dissociation</option>
71 <option value=""></option> 71 <option value="any">any</option>
72 <expand macro="list_string_san" name="select_activation"/> 72 <expand macro="list_string_san" name="select_activation"/>
73 </param> 73 </param>
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=""/> 74 <param name="reporter_mass_shift" argument="-extraction:reporter_mass_shift" type="float" min="0.0001" max="0.5" value="0.002" label="Allowed shift (left to right) in Th from the expected position" help=""/>
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"/> 75 <param name="min_precursor_intensity" argument="-extraction:min_precursor_intensity" type="float" 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"/>
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=""/> 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=""/>
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="min_reporter_intensity" argument="-extraction:min_reporter_intensity" type="float" min="0.0" value="0.0" label="Minimum intensity of the individual reporter ions to be extracted" help=""/>
78 <param name="discard_low_intensity_quantifications" argument="-extraction:discard_low_intensity_quantifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'" help=""/> 78 <param name="discard_low_intensity_quantifications" argument="-extraction:discard_low_intensity_quantifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'" help=""/>
79 <param name="min_precursor_purity" argument="-extraction:min_precursor_purity" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precurso" help=""/> 79 <param name="min_precursor_purity" argument="-extraction:min_precursor_purity" type="float" min="0.0" max="1.0" value="0.0" label="Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected 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=""/> 80 <param name="precursor_isotope_deviation" argument="-extraction:precursor_isotope_deviation" type="float" 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=""/>
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"/> 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"/>
82 </section> 82 </section>
83 <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">
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=""> 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="">
85 <expand macro="list_string_san" name="channel_114_description"/> 85 <expand macro="list_string_san" name="channel_114_description"/>
91 <expand macro="list_string_san" name="channel_116_description"/> 91 <expand macro="list_string_san" name="channel_116_description"/>
92 </param> 92 </param>
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=""> 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="">
94 <expand macro="list_string_san" name="channel_117_description"/> 94 <expand macro="list_string_san" name="channel_117_description"/>
95 </param> 95 </param>
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=""/> 96 <param name="reference_channel" argument="-itraq4plex:reference_channel" type="integer" min="114" max="117" value="114" label="Number of the reference channel (114-117)" help=""/>
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)"> 97 <param name="correction_matrix" argument="-itraq4plex:correction_matrix" type="text" 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)">
98 <expand macro="list_string_val" name="correction_matrix"/> 98 <expand macro="list_string_val" name="correction_matrix"/>
99 <expand macro="list_string_san" name="correction_matrix"/> 99 <expand macro="list_string_san" name="correction_matrix"/>
100 </param> 100 </param>
101 </section> 101 </section>
102 <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">
122 <expand macro="list_string_san" name="channel_119_description"/> 122 <expand macro="list_string_san" name="channel_119_description"/>
123 </param> 123 </param>
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=""> 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="">
125 <expand macro="list_string_san" name="channel_121_description"/> 125 <expand macro="list_string_san" name="channel_121_description"/>
126 </param> 126 </param>
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"/> 127 <param name="reference_channel" argument="-itraq8plex:reference_channel" type="integer" min="113" max="121" value="113" label="Number of the reference channel (113-121)" help="Please note that 120 is not valid"/>
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)"> 128 <param name="correction_matrix" argument="-itraq8plex:correction_matrix" type="text" 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)">
129 <expand macro="list_string_val" name="correction_matrix"/> 129 <expand macro="list_string_val" name="correction_matrix"/>
130 <expand macro="list_string_san" name="correction_matrix"/> 130 <expand macro="list_string_san" name="correction_matrix"/>
131 </param> 131 </param>
132 </section> 132 </section>
133 <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">
163 <expand macro="list_string_san" name="channel_130C_description"/> 163 <expand macro="list_string_san" name="channel_130C_description"/>
164 </param> 164 </param>
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=""> 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="">
166 <expand macro="list_string_san" name="channel_131_description"/> 166 <expand macro="list_string_san" name="channel_131_description"/>
167 </param> 167 </param>
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=""> 168 <param name="reference_channel" argument="-tmt10plex:reference_channel" type="select" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" help="">
169 <option value="126" selected="true">126</option> 169 <option value="126" selected="true">126</option>
170 <option value="127N">127N</option> 170 <option value="127N">127N</option>
171 <option value="127C">127C</option> 171 <option value="127C">127C</option>
172 <option value="128N">128N</option> 172 <option value="128N">128N</option>
173 <option value="128C">128C</option> 173 <option value="128C">128C</option>
176 <option value="130N">130N</option> 176 <option value="130N">130N</option>
177 <option value="130C">130C</option> 177 <option value="130C">130C</option>
178 <option value="131">131</option> 178 <option value="131">131</option>
179 <expand macro="list_string_san" name="reference_channel"/> 179 <expand macro="list_string_san" name="reference_channel"/>
180 </param> 180 </param>
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)"> 181 <param name="correction_matrix" argument="-tmt10plex:correction_matrix" type="text" 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)">
182 <expand macro="list_string_val" name="correction_matrix"/> 182 <expand macro="list_string_val" name="correction_matrix"/>
183 <expand macro="list_string_san" name="correction_matrix"/> 183 <expand macro="list_string_san" name="correction_matrix"/>
184 </param> 184 </param>
185 </section> 185 </section>
186 <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">
215 <expand macro="list_string_san" name="channel_131N_description"/> 215 <expand macro="list_string_san" name="channel_131N_description"/>
216 </param> 216 </param>
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=""> 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="">
218 <expand macro="list_string_san" name="channel_131C_description"/> 218 <expand macro="list_string_san" name="channel_131C_description"/>
219 </param> 219 </param>
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=""> 220 <param name="reference_channel" argument="-tmt11plex:reference_channel" type="select" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help="">
221 <option value="126" selected="true">126</option> 221 <option value="126" selected="true">126</option>
222 <option value="127N">127N</option> 222 <option value="127N">127N</option>
223 <option value="127C">127C</option> 223 <option value="127C">127C</option>
224 <option value="128N">128N</option> 224 <option value="128N">128N</option>
225 <option value="128C">128C</option> 225 <option value="128C">128C</option>
229 <option value="130C">130C</option> 229 <option value="130C">130C</option>
230 <option value="131N">131N</option> 230 <option value="131N">131N</option>
231 <option value="131C">131C</option> 231 <option value="131C">131C</option>
232 <expand macro="list_string_san" name="reference_channel"/> 232 <expand macro="list_string_san" name="reference_channel"/>
233 </param> 233 </param>
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)"> 234 <param name="correction_matrix" argument="-tmt11plex:correction_matrix" type="text" 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)">
235 <expand macro="list_string_val" name="correction_matrix"/> 235 <expand macro="list_string_val" name="correction_matrix"/>
236 <expand macro="list_string_san" name="correction_matrix"/> 236 <expand macro="list_string_san" name="correction_matrix"/>
237 </param> 237 </param>
238 </section> 238 </section>
239 <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">
283 <expand macro="list_string_san" name="channel_133C_description"/> 283 <expand macro="list_string_san" name="channel_133C_description"/>
284 </param> 284 </param>
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=""> 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="">
286 <expand macro="list_string_san" name="channel_134N_description"/> 286 <expand macro="list_string_san" name="channel_134N_description"/>
287 </param> 287 </param>
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=""> 288 <param name="reference_channel" argument="-tmt16plex:reference_channel" type="select" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N)" help="">
289 <option value="126" selected="true">126</option> 289 <option value="126" selected="true">126</option>
290 <option value="127N">127N</option> 290 <option value="127N">127N</option>
291 <option value="127C">127C</option> 291 <option value="127C">127C</option>
292 <option value="128N">128N</option> 292 <option value="128N">128N</option>
293 <option value="128C">128C</option> 293 <option value="128C">128C</option>
302 <option value="133N">133N</option> 302 <option value="133N">133N</option>
303 <option value="133C">133C</option> 303 <option value="133C">133C</option>
304 <option value="134N">134N</option> 304 <option value="134N">134N</option>
305 <expand macro="list_string_san" name="reference_channel"/> 305 <expand macro="list_string_san" name="reference_channel"/>
306 </param> 306 </param>
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)"> 307 <param name="correction_matrix" argument="-tmt16plex:correction_matrix" type="text" value="&quot;NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32&quot; &quot;NA/NA / NA/0.78 / NA/9.41 / NA/0.33&quot; &quot;NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27&quot; &quot;NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26&quot; &quot;0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15&quot; &quot;0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15&quot; &quot;0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09&quot; &quot;0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10&quot; &quot;0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06&quot; &quot;0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12&quot; &quot;0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04&quot; &quot;0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00&quot; &quot;0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00&quot; &quot;0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03&quot; &quot;0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA&quot; &quot;0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA&quot;" label="Correction matrix for isotope distributions in percent from the Thermo data sheet (see documentation); Please provide 16 entries (rows), separated by comma, where each entry contains 8 values in the following format: &lt;-2C13&gt;/&lt;-N15-C13&gt;/&lt;-C13&gt;/&lt;-N15&gt;/&lt;+N15&gt;/&lt;+C13&gt;/&lt;+N15+C13&gt;/&lt;+2C13" help="e.g. one row may look like this: 'NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26'. You may use whitespaces at your leisure to ease reading (space separated list, in order to allow for spaces in list items surround them by single quotes)">
308 <expand macro="list_string_val" name="correction_matrix"/>
309 <expand macro="list_string_san" name="correction_matrix"/>
310 </param>
311 </section>
312 <section name="tmt18plex" title="Algorithm parameters for TMT 18-plex" help="" expanded="false">
313 <param name="channel_126_description" argument="-tmt18plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help="">
314 <expand macro="list_string_san" name="channel_126_description"/>
315 </param>
316 <param name="channel_127N_description" argument="-tmt18plex:channel_127N_description" type="text" optional="true" value="" label="Description for the content of the 127N channel" help="">
317 <expand macro="list_string_san" name="channel_127N_description"/>
318 </param>
319 <param name="channel_127C_description" argument="-tmt18plex:channel_127C_description" type="text" optional="true" value="" label="Description for the content of the 127C channel" help="">
320 <expand macro="list_string_san" name="channel_127C_description"/>
321 </param>
322 <param name="channel_128N_description" argument="-tmt18plex:channel_128N_description" type="text" optional="true" value="" label="Description for the content of the 128N channel" help="">
323 <expand macro="list_string_san" name="channel_128N_description"/>
324 </param>
325 <param name="channel_128C_description" argument="-tmt18plex:channel_128C_description" type="text" optional="true" value="" label="Description for the content of the 128C channel" help="">
326 <expand macro="list_string_san" name="channel_128C_description"/>
327 </param>
328 <param name="channel_129N_description" argument="-tmt18plex:channel_129N_description" type="text" optional="true" value="" label="Description for the content of the 129N channel" help="">
329 <expand macro="list_string_san" name="channel_129N_description"/>
330 </param>
331 <param name="channel_129C_description" argument="-tmt18plex:channel_129C_description" type="text" optional="true" value="" label="Description for the content of the 129C channel" help="">
332 <expand macro="list_string_san" name="channel_129C_description"/>
333 </param>
334 <param name="channel_130N_description" argument="-tmt18plex:channel_130N_description" type="text" optional="true" value="" label="Description for the content of the 130N channel" help="">
335 <expand macro="list_string_san" name="channel_130N_description"/>
336 </param>
337 <param name="channel_130C_description" argument="-tmt18plex:channel_130C_description" type="text" optional="true" value="" label="Description for the content of the 130C channel" help="">
338 <expand macro="list_string_san" name="channel_130C_description"/>
339 </param>
340 <param name="channel_131N_description" argument="-tmt18plex:channel_131N_description" type="text" optional="true" value="" label="Description for the content of the 131N channel" help="">
341 <expand macro="list_string_san" name="channel_131N_description"/>
342 </param>
343 <param name="channel_131C_description" argument="-tmt18plex:channel_131C_description" type="text" optional="true" value="" label="Description for the content of the 131C channel" help="">
344 <expand macro="list_string_san" name="channel_131C_description"/>
345 </param>
346 <param name="channel_132N_description" argument="-tmt18plex:channel_132N_description" type="text" optional="true" value="" label="Description for the content of the 132N channel" help="">
347 <expand macro="list_string_san" name="channel_132N_description"/>
348 </param>
349 <param name="channel_132C_description" argument="-tmt18plex:channel_132C_description" type="text" optional="true" value="" label="Description for the content of the 132C channel" help="">
350 <expand macro="list_string_san" name="channel_132C_description"/>
351 </param>
352 <param name="channel_133N_description" argument="-tmt18plex:channel_133N_description" type="text" optional="true" value="" label="Description for the content of the 133N channel" help="">
353 <expand macro="list_string_san" name="channel_133N_description"/>
354 </param>
355 <param name="channel_133C_description" argument="-tmt18plex:channel_133C_description" type="text" optional="true" value="" label="Description for the content of the 133C channel" help="">
356 <expand macro="list_string_san" name="channel_133C_description"/>
357 </param>
358 <param name="channel_134N_description" argument="-tmt18plex:channel_134N_description" type="text" optional="true" value="" label="Description for the content of the 134N channel" help="">
359 <expand macro="list_string_san" name="channel_134N_description"/>
360 </param>
361 <param name="channel_134C_description" argument="-tmt18plex:channel_134C_description" type="text" optional="true" value="" label="Description for the content of the 134C channel" help="">
362 <expand macro="list_string_san" name="channel_134C_description"/>
363 </param>
364 <param name="channel_135N_description" argument="-tmt18plex:channel_135N_description" type="text" optional="true" value="" label="Description for the content of the 135N channel" help="">
365 <expand macro="list_string_san" name="channel_135N_description"/>
366 </param>
367 <param name="reference_channel" argument="-tmt18plex:reference_channel" type="select" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N, 134C, 135N)" help="">
368 <option value="126" selected="true">126</option>
369 <option value="127N">127N</option>
370 <option value="127C">127C</option>
371 <option value="128N">128N</option>
372 <option value="128C">128C</option>
373 <option value="129N">129N</option>
374 <option value="129C">129C</option>
375 <option value="130N">130N</option>
376 <option value="130C">130C</option>
377 <option value="131N">131N</option>
378 <option value="131C">131C</option>
379 <option value="132N">132N</option>
380 <option value="132C">132C</option>
381 <option value="133N">133N</option>
382 <option value="133C">133C</option>
383 <option value="134N">134N</option>
384 <option value="134C">134C</option>
385 <option value="135N">135N</option>
386 <expand macro="list_string_san" name="reference_channel"/>
387 </param>
388 <param name="correction_matrix" argument="-tmt18plex:correction_matrix" type="text" value="&quot;NA/NA /NA/NA /0.31/9.09 /0.02/0.32&quot; &quot;NA/NA /NA/0.78 /NA/9.41 /NA/0.33&quot; &quot;NA/NA /0.93/NA /0.35/8.63 /0.01/0.27&quot; &quot;NA/0.00 /0.82/0.65 /NA/8.13 /NA/0.26&quot; &quot;0.00/NA /1.47/NA /0.34/6.91 /0.00/0.15&quot; &quot;0.00/0.00 /1.46/1.28 /NA/6.86 /NA/0.15&quot; &quot;0.13/NA /2.59/NA /0.32/6.07 /0.1/0.09&quot; &quot;0.13/0.00 /2.41/0.27 /NA/5.58 /NA/0.10&quot; &quot;0.04/NA /3.10/NA /0.42/4.82 /0.02/0.06&quot; &quot;0.03/0.00 /2.78/0.63 /NA/4.57 /NA/0.12&quot; &quot;0.08/NA /3.90/NA /0.47/3.57 /0.00/0.04&quot; &quot;0.15/0.01 /3.58/0.72 /NA/1.80 /NA/0.00&quot; &quot;0.11/NA /4.55/NA /0.43/1.86 /0.00/0.00&quot; &quot;0.07/0.01 /3.14/0.73 /NA/3.40 /NA/0.03&quot; &quot;0.22/NA /4.96/NA /0.34/1.03 /0.00/NA&quot; &quot;0.30/0.03 /5.49/0.62 /NA/1.14 /NA/NA&quot; &quot;0.14/NA /5.81/NA /0.31/NA /NA/NA&quot; &quot;0.19/0.02 /5.42/0.36 /NA/NA /NA/NA&quot;" label="Correction matrix for isotope distributions in percent from the Thermo data sheet (see documentation); Please provide 18 entries (rows), separated by comma, where each entry contains 8 values in the following format: &lt;-2C13&gt;/&lt;-N15-C13&gt;/&lt;-C13&gt;/&lt;-N15&gt;/&lt;+N15&gt;/&lt;+C13&gt;/&lt;+N15+C13&gt;/&lt;+2C13" help="e.g. one row may look like this: 'NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26'. You may use whitespaces at your leisure to ease reading (space separated list, in order to allow for spaces in list items surround them by single quotes)">
308 <expand macro="list_string_val" name="correction_matrix"/> 389 <expand macro="list_string_val" name="correction_matrix"/>
309 <expand macro="list_string_san" name="correction_matrix"/> 390 <expand macro="list_string_san" name="correction_matrix"/>
310 </param> 391 </param>
311 </section> 392 </section>
312 <section name="tmt6plex" title="Algorithm parameters for TMT 6-plex" help="" expanded="false"> 393 <section name="tmt6plex" title="Algorithm parameters for TMT 6-plex" help="" expanded="false">
326 <expand macro="list_string_san" name="channel_130_description"/> 407 <expand macro="list_string_san" name="channel_130_description"/>
327 </param> 408 </param>
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=""> 409 <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="">
329 <expand macro="list_string_san" name="channel_131_description"/> 410 <expand macro="list_string_san" name="channel_131_description"/>
330 </param> 411 </param>
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=""/> 412 <param name="reference_channel" argument="-tmt6plex:reference_channel" type="integer" min="126" max="131" value="126" label="Number of the reference channel (126-131)" help=""/>
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)"> 413 <param name="correction_matrix" argument="-tmt6plex:correction_matrix" type="text" 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)">
333 <expand macro="list_string_val" name="correction_matrix"/> 414 <expand macro="list_string_val" name="correction_matrix"/>
334 <expand macro="list_string_san" name="correction_matrix"/> 415 <expand macro="list_string_san" name="correction_matrix"/>
335 </param> 416 </param>
336 </section> 417 </section>
337 <expand macro="adv_opts_macro"> 418 <expand macro="adv_opts_macro">
338 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 419 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
339 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 420 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
340 <expand macro="list_string_san" name="test"/> 421 <expand macro="list_string_san" name="test"/>
341 </param> 422 </param>
342 </expand> 423 </expand>
343 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 424 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
344 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 425 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
348 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> 429 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
349 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 430 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
350 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 431 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
351 </data> 432 </data>
352 </outputs> 433 </outputs>
353 <tests><!-- TOPP_IsobaricAnalyzer_1 --> 434 <tests>
435 <!-- TOPP_IsobaricAnalyzer_1 -->
354 <test expect_num_outputs="2"> 436 <test expect_num_outputs="2">
355 <section name="adv_opts"> 437 <section name="adv_opts">
356 <param name="force" value="false"/> 438 <param name="force" value="false"/>
357 <param name="test" value="true"/> 439 <param name="test" value="true"/>
358 </section> 440 </section>
359 <param name="type" value="itraq4plex"/> 441 <param name="type" value="itraq4plex"/>
360 <param name="in" value="IsobaricAnalyzer_input_1.mzML"/> 442 <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"/> 443 <output name="out" value="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
362 <section name="extraction"> 444 <section name="extraction">
363 <param name="select_activation"/> 445 <param name="select_activation" value="any"/>
364 <param name="reporter_mass_shift" value="0.1"/> 446 <param name="reporter_mass_shift" value="0.1"/>
365 <param name="min_precursor_intensity" value="1.0"/> 447 <param name="min_precursor_intensity" value="1.0"/>
366 <param name="keep_unannotated_precursor" value="true"/> 448 <param name="keep_unannotated_precursor" value="true"/>
367 <param name="min_reporter_intensity" value="0.0"/> 449 <param name="min_reporter_intensity" value="0.0"/>
368 <param name="discard_low_intensity_quantifications" value="false"/> 450 <param name="discard_low_intensity_quantifications" value="false"/>
439 <param name="channel_132C_description" value=""/> 521 <param name="channel_132C_description" value=""/>
440 <param name="channel_133N_description" value=""/> 522 <param name="channel_133N_description" value=""/>
441 <param name="channel_133C_description" value=""/> 523 <param name="channel_133C_description" value=""/>
442 <param name="channel_134N_description" value=""/> 524 <param name="channel_134N_description" value=""/>
443 <param name="reference_channel" value="126"/> 525 <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;"/> 526 <param name="correction_matrix" value="&quot;NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32&quot; &quot;NA/NA / NA/0.78 / NA/9.41 / NA/0.33&quot; &quot;NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27&quot; &quot;NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26&quot; &quot;0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15&quot; &quot;0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15&quot; &quot;0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09&quot; &quot;0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10&quot; &quot;0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06&quot; &quot;0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12&quot; &quot;0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04&quot; &quot;0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00&quot; &quot;0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00&quot; &quot;0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03&quot; &quot;0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA&quot; &quot;0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA&quot;"/>
527 </section>
528 <section name="tmt18plex">
529 <param name="channel_126_description" value=""/>
530 <param name="channel_127N_description" value=""/>
531 <param name="channel_127C_description" value=""/>
532 <param name="channel_128N_description" value=""/>
533 <param name="channel_128C_description" value=""/>
534 <param name="channel_129N_description" value=""/>
535 <param name="channel_129C_description" value=""/>
536 <param name="channel_130N_description" value=""/>
537 <param name="channel_130C_description" value=""/>
538 <param name="channel_131N_description" value=""/>
539 <param name="channel_131C_description" value=""/>
540 <param name="channel_132N_description" value=""/>
541 <param name="channel_132C_description" value=""/>
542 <param name="channel_133N_description" value=""/>
543 <param name="channel_133C_description" value=""/>
544 <param name="channel_134N_description" value=""/>
545 <param name="channel_134C_description" value=""/>
546 <param name="channel_135N_description" value=""/>
547 <param name="reference_channel" value="126"/>
548 <param name="correction_matrix" value="&quot;NA/NA /NA/NA /0.31/9.09 /0.02/0.32&quot; &quot;NA/NA /NA/0.78 /NA/9.41 /NA/0.33&quot; &quot;NA/NA /0.93/NA /0.35/8.63 /0.01/0.27&quot; &quot;NA/0.00 /0.82/0.65 /NA/8.13 /NA/0.26&quot; &quot;0.00/NA /1.47/NA /0.34/6.91 /0.00/0.15&quot; &quot;0.00/0.00 /1.46/1.28 /NA/6.86 /NA/0.15&quot; &quot;0.13/NA /2.59/NA /0.32/6.07 /0.1/0.09&quot; &quot;0.13/0.00 /2.41/0.27 /NA/5.58 /NA/0.10&quot; &quot;0.04/NA /3.10/NA /0.42/4.82 /0.02/0.06&quot; &quot;0.03/0.00 /2.78/0.63 /NA/4.57 /NA/0.12&quot; &quot;0.08/NA /3.90/NA /0.47/3.57 /0.00/0.04&quot; &quot;0.15/0.01 /3.58/0.72 /NA/1.80 /NA/0.00&quot; &quot;0.11/NA /4.55/NA /0.43/1.86 /0.00/0.00&quot; &quot;0.07/0.01 /3.14/0.73 /NA/3.40 /NA/0.03&quot; &quot;0.22/NA /4.96/NA /0.34/1.03 /0.00/NA&quot; &quot;0.30/0.03 /5.49/0.62 /NA/1.14 /NA/NA&quot; &quot;0.14/NA /5.81/NA /0.31/NA /NA/NA&quot; &quot;0.19/0.02 /5.42/0.36 /NA/NA /NA/NA&quot;"/>
445 </section> 549 </section>
446 <section name="tmt6plex"> 550 <section name="tmt6plex">
447 <param name="channel_126_description" value=""/> 551 <param name="channel_126_description" value=""/>
448 <param name="channel_127_description" value=""/> 552 <param name="channel_127_description" value=""/>
449 <param name="channel_128_description" value=""/> 553 <param name="channel_128_description" value=""/>
457 <output name="ctd_out" ftype="xml"> 561 <output name="ctd_out" ftype="xml">
458 <assert_contents> 562 <assert_contents>
459 <is_valid_xml/> 563 <is_valid_xml/>
460 </assert_contents> 564 </assert_contents>
461 </output> 565 </output>
566 <assert_stdout>
567 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
568 </assert_stdout>
462 </test> 569 </test>
463 <!-- TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1 --> 570 <!-- TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1 -->
464 <test expect_num_outputs="2"> 571 <test expect_num_outputs="2">
465 <section name="adv_opts"> 572 <section name="adv_opts">
466 <param name="force" value="false"/> 573 <param name="force" value="false"/>
467 <param name="test" value="true"/> 574 <param name="test" value="true"/>
468 </section> 575 </section>
469 <param name="type" value="itraq4plex"/> 576 <param name="type" value="itraq4plex"/>
470 <param name="in" value="TMTTenPlexMethod_test.mzML"/> 577 <param name="in" value="TMTTenPlexMethod_test.mzML"/>
471 <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 578 <output name="out" value="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
472 <section name="extraction"> 579 <section name="extraction">
473 <param name="select_activation" value="auto"/> 580 <param name="select_activation" value="auto"/>
474 <param name="reporter_mass_shift" value="0.002"/> 581 <param name="reporter_mass_shift" value="0.002"/>
475 <param name="min_precursor_intensity" value="1.0"/> 582 <param name="min_precursor_intensity" value="1.0"/>
476 <param name="keep_unannotated_precursor" value="true"/> 583 <param name="keep_unannotated_precursor" value="true"/>
549 <param name="channel_132C_description" value=""/> 656 <param name="channel_132C_description" value=""/>
550 <param name="channel_133N_description" value=""/> 657 <param name="channel_133N_description" value=""/>
551 <param name="channel_133C_description" value=""/> 658 <param name="channel_133C_description" value=""/>
552 <param name="channel_134N_description" value=""/> 659 <param name="channel_134N_description" value=""/>
553 <param name="reference_channel" value="126"/> 660 <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;"/> 661 <param name="correction_matrix" value="&quot;NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32&quot; &quot;NA/NA / NA/0.78 / NA/9.41 / NA/0.33&quot; &quot;NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27&quot; &quot;NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26&quot; &quot;0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15&quot; &quot;0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15&quot; &quot;0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09&quot; &quot;0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10&quot; &quot;0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06&quot; &quot;0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12&quot; &quot;0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04&quot; &quot;0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00&quot; &quot;0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00&quot; &quot;0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03&quot; &quot;0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA&quot; &quot;0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA&quot;"/>
662 </section>
663 <section name="tmt18plex">
664 <param name="channel_126_description" value=""/>
665 <param name="channel_127N_description" value=""/>
666 <param name="channel_127C_description" value=""/>
667 <param name="channel_128N_description" value=""/>
668 <param name="channel_128C_description" value=""/>
669 <param name="channel_129N_description" value=""/>
670 <param name="channel_129C_description" value=""/>
671 <param name="channel_130N_description" value=""/>
672 <param name="channel_130C_description" value=""/>
673 <param name="channel_131N_description" value=""/>
674 <param name="channel_131C_description" value=""/>
675 <param name="channel_132N_description" value=""/>
676 <param name="channel_132C_description" value=""/>
677 <param name="channel_133N_description" value=""/>
678 <param name="channel_133C_description" value=""/>
679 <param name="channel_134N_description" value=""/>
680 <param name="channel_134C_description" value=""/>
681 <param name="channel_135N_description" value=""/>
682 <param name="reference_channel" value="126"/>
683 <param name="correction_matrix" value="&quot;NA/NA /NA/NA /0.31/9.09 /0.02/0.32&quot; &quot;NA/NA /NA/0.78 /NA/9.41 /NA/0.33&quot; &quot;NA/NA /0.93/NA /0.35/8.63 /0.01/0.27&quot; &quot;NA/0.00 /0.82/0.65 /NA/8.13 /NA/0.26&quot; &quot;0.00/NA /1.47/NA /0.34/6.91 /0.00/0.15&quot; &quot;0.00/0.00 /1.46/1.28 /NA/6.86 /NA/0.15&quot; &quot;0.13/NA /2.59/NA /0.32/6.07 /0.1/0.09&quot; &quot;0.13/0.00 /2.41/0.27 /NA/5.58 /NA/0.10&quot; &quot;0.04/NA /3.10/NA /0.42/4.82 /0.02/0.06&quot; &quot;0.03/0.00 /2.78/0.63 /NA/4.57 /NA/0.12&quot; &quot;0.08/NA /3.90/NA /0.47/3.57 /0.00/0.04&quot; &quot;0.15/0.01 /3.58/0.72 /NA/1.80 /NA/0.00&quot; &quot;0.11/NA /4.55/NA /0.43/1.86 /0.00/0.00&quot; &quot;0.07/0.01 /3.14/0.73 /NA/3.40 /NA/0.03&quot; &quot;0.22/NA /4.96/NA /0.34/1.03 /0.00/NA&quot; &quot;0.30/0.03 /5.49/0.62 /NA/1.14 /NA/NA&quot; &quot;0.14/NA /5.81/NA /0.31/NA /NA/NA&quot; &quot;0.19/0.02 /5.42/0.36 /NA/NA /NA/NA&quot;"/>
555 </section> 684 </section>
556 <section name="tmt6plex"> 685 <section name="tmt6plex">
557 <param name="channel_126_description" value=""/> 686 <param name="channel_126_description" value=""/>
558 <param name="channel_127_description" value=""/> 687 <param name="channel_127_description" value=""/>
559 <param name="channel_128_description" value=""/> 688 <param name="channel_128_description" value=""/>
567 <output name="ctd_out" ftype="xml"> 696 <output name="ctd_out" ftype="xml">
568 <assert_contents> 697 <assert_contents>
569 <is_valid_xml/> 698 <is_valid_xml/>
570 </assert_contents> 699 </assert_contents>
571 </output> 700 </output>
701 <assert_stdout>
702 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
703 </assert_stdout>
572 </test> 704 </test>
573 <!-- TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1 --> 705 <!-- TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1 -->
574 <test expect_num_outputs="2"> 706 <test expect_num_outputs="2">
575 <section name="adv_opts"> 707 <section name="adv_opts">
576 <param name="force" value="false"/> 708 <param name="force" value="false"/>
577 <param name="test" value="true"/> 709 <param name="test" value="true"/>
578 </section> 710 </section>
579 <param name="type" value="itraq4plex"/> 711 <param name="type" value="itraq4plex"/>
580 <param name="in" value="TMTTenPlexMethod_test.mzML"/> 712 <param name="in" value="TMTTenPlexMethod_test.mzML"/>
581 <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 713 <output name="out" value="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
582 <section name="extraction"> 714 <section name="extraction">
583 <param name="select_activation" value="auto"/> 715 <param name="select_activation" value="auto"/>
584 <param name="reporter_mass_shift" value="0.002"/> 716 <param name="reporter_mass_shift" value="0.002"/>
585 <param name="min_precursor_intensity" value="1.0"/> 717 <param name="min_precursor_intensity" value="1.0"/>
586 <param name="keep_unannotated_precursor" value="true"/> 718 <param name="keep_unannotated_precursor" value="true"/>
659 <param name="channel_132C_description" value=""/> 791 <param name="channel_132C_description" value=""/>
660 <param name="channel_133N_description" value=""/> 792 <param name="channel_133N_description" value=""/>
661 <param name="channel_133C_description" value=""/> 793 <param name="channel_133C_description" value=""/>
662 <param name="channel_134N_description" value=""/> 794 <param name="channel_134N_description" value=""/>
663 <param name="reference_channel" value="126"/> 795 <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;"/> 796 <param name="correction_matrix" value="&quot;NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32&quot; &quot;NA/NA / NA/0.78 / NA/9.41 / NA/0.33&quot; &quot;NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27&quot; &quot;NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26&quot; &quot;0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15&quot; &quot;0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15&quot; &quot;0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09&quot; &quot;0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10&quot; &quot;0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06&quot; &quot;0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12&quot; &quot;0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04&quot; &quot;0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00&quot; &quot;0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00&quot; &quot;0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03&quot; &quot;0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA&quot; &quot;0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA&quot;"/>
797 </section>
798 <section name="tmt18plex">
799 <param name="channel_126_description" value=""/>
800 <param name="channel_127N_description" value=""/>
801 <param name="channel_127C_description" value=""/>
802 <param name="channel_128N_description" value=""/>
803 <param name="channel_128C_description" value=""/>
804 <param name="channel_129N_description" value=""/>
805 <param name="channel_129C_description" value=""/>
806 <param name="channel_130N_description" value=""/>
807 <param name="channel_130C_description" value=""/>
808 <param name="channel_131N_description" value=""/>
809 <param name="channel_131C_description" value=""/>
810 <param name="channel_132N_description" value=""/>
811 <param name="channel_132C_description" value=""/>
812 <param name="channel_133N_description" value=""/>
813 <param name="channel_133C_description" value=""/>
814 <param name="channel_134N_description" value=""/>
815 <param name="channel_134C_description" value=""/>
816 <param name="channel_135N_description" value=""/>
817 <param name="reference_channel" value="126"/>
818 <param name="correction_matrix" value="&quot;NA/NA /NA/NA /0.31/9.09 /0.02/0.32&quot; &quot;NA/NA /NA/0.78 /NA/9.41 /NA/0.33&quot; &quot;NA/NA /0.93/NA /0.35/8.63 /0.01/0.27&quot; &quot;NA/0.00 /0.82/0.65 /NA/8.13 /NA/0.26&quot; &quot;0.00/NA /1.47/NA /0.34/6.91 /0.00/0.15&quot; &quot;0.00/0.00 /1.46/1.28 /NA/6.86 /NA/0.15&quot; &quot;0.13/NA /2.59/NA /0.32/6.07 /0.1/0.09&quot; &quot;0.13/0.00 /2.41/0.27 /NA/5.58 /NA/0.10&quot; &quot;0.04/NA /3.10/NA /0.42/4.82 /0.02/0.06&quot; &quot;0.03/0.00 /2.78/0.63 /NA/4.57 /NA/0.12&quot; &quot;0.08/NA /3.90/NA /0.47/3.57 /0.00/0.04&quot; &quot;0.15/0.01 /3.58/0.72 /NA/1.80 /NA/0.00&quot; &quot;0.11/NA /4.55/NA /0.43/1.86 /0.00/0.00&quot; &quot;0.07/0.01 /3.14/0.73 /NA/3.40 /NA/0.03&quot; &quot;0.22/NA /4.96/NA /0.34/1.03 /0.00/NA&quot; &quot;0.30/0.03 /5.49/0.62 /NA/1.14 /NA/NA&quot; &quot;0.14/NA /5.81/NA /0.31/NA /NA/NA&quot; &quot;0.19/0.02 /5.42/0.36 /NA/NA /NA/NA&quot;"/>
665 </section> 819 </section>
666 <section name="tmt6plex"> 820 <section name="tmt6plex">
667 <param name="channel_126_description" value=""/> 821 <param name="channel_126_description" value=""/>
668 <param name="channel_127_description" value=""/> 822 <param name="channel_127_description" value=""/>
669 <param name="channel_128_description" value=""/> 823 <param name="channel_128_description" value=""/>
677 <output name="ctd_out" ftype="xml"> 831 <output name="ctd_out" ftype="xml">
678 <assert_contents> 832 <assert_contents>
679 <is_valid_xml/> 833 <is_valid_xml/>
680 </assert_contents> 834 </assert_contents>
681 </output> 835 </output>
836 <assert_stdout>
837 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
838 </assert_stdout>
682 </test> 839 </test>
683 <!-- TOPP_IsobaricAnalyzer_MS3TMT10Plex_1 --> 840 <!-- TOPP_IsobaricAnalyzer_MS3TMT10Plex_1 -->
684 <test expect_num_outputs="2"> 841 <test expect_num_outputs="2">
685 <section name="adv_opts"> 842 <section name="adv_opts">
686 <param name="force" value="false"/> 843 <param name="force" value="false"/>
687 <param name="test" value="true"/> 844 <param name="test" value="true"/>
688 </section> 845 </section>
689 <param name="type" value="tmt10plex"/> 846 <param name="type" value="tmt10plex"/>
690 <param name="in" value="MS3_nonHierarchical.mzML"/> 847 <param name="in" value="MS3_nonHierarchical.mzML"/>
691 <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 848 <output name="out" value="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
692 <section name="extraction"> 849 <section name="extraction">
693 <param name="select_activation" value="Collision-induced dissociation"/> 850 <param name="select_activation" value="Collision-induced dissociation"/>
694 <param name="reporter_mass_shift" value="0.002"/> 851 <param name="reporter_mass_shift" value="0.002"/>
695 <param name="min_precursor_intensity" value="1.0"/> 852 <param name="min_precursor_intensity" value="1.0"/>
696 <param name="keep_unannotated_precursor" value="true"/> 853 <param name="keep_unannotated_precursor" value="true"/>
769 <param name="channel_132C_description" value=""/> 926 <param name="channel_132C_description" value=""/>
770 <param name="channel_133N_description" value=""/> 927 <param name="channel_133N_description" value=""/>
771 <param name="channel_133C_description" value=""/> 928 <param name="channel_133C_description" value=""/>
772 <param name="channel_134N_description" value=""/> 929 <param name="channel_134N_description" value=""/>
773 <param name="reference_channel" value="126"/> 930 <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;"/> 931 <param name="correction_matrix" value="&quot;NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32&quot; &quot;NA/NA / NA/0.78 / NA/9.41 / NA/0.33&quot; &quot;NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27&quot; &quot;NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26&quot; &quot;0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15&quot; &quot;0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15&quot; &quot;0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09&quot; &quot;0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10&quot; &quot;0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06&quot; &quot;0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12&quot; &quot;0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04&quot; &quot;0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00&quot; &quot;0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00&quot; &quot;0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03&quot; &quot;0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA&quot; &quot;0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA&quot;"/>
932 </section>
933 <section name="tmt18plex">
934 <param name="channel_126_description" value=""/>
935 <param name="channel_127N_description" value=""/>
936 <param name="channel_127C_description" value=""/>
937 <param name="channel_128N_description" value=""/>
938 <param name="channel_128C_description" value=""/>
939 <param name="channel_129N_description" value=""/>
940 <param name="channel_129C_description" value=""/>
941 <param name="channel_130N_description" value=""/>
942 <param name="channel_130C_description" value=""/>
943 <param name="channel_131N_description" value=""/>
944 <param name="channel_131C_description" value=""/>
945 <param name="channel_132N_description" value=""/>
946 <param name="channel_132C_description" value=""/>
947 <param name="channel_133N_description" value=""/>
948 <param name="channel_133C_description" value=""/>
949 <param name="channel_134N_description" value=""/>
950 <param name="channel_134C_description" value=""/>
951 <param name="channel_135N_description" value=""/>
952 <param name="reference_channel" value="126"/>
953 <param name="correction_matrix" value="&quot;NA/NA /NA/NA /0.31/9.09 /0.02/0.32&quot; &quot;NA/NA /NA/0.78 /NA/9.41 /NA/0.33&quot; &quot;NA/NA /0.93/NA /0.35/8.63 /0.01/0.27&quot; &quot;NA/0.00 /0.82/0.65 /NA/8.13 /NA/0.26&quot; &quot;0.00/NA /1.47/NA /0.34/6.91 /0.00/0.15&quot; &quot;0.00/0.00 /1.46/1.28 /NA/6.86 /NA/0.15&quot; &quot;0.13/NA /2.59/NA /0.32/6.07 /0.1/0.09&quot; &quot;0.13/0.00 /2.41/0.27 /NA/5.58 /NA/0.10&quot; &quot;0.04/NA /3.10/NA /0.42/4.82 /0.02/0.06&quot; &quot;0.03/0.00 /2.78/0.63 /NA/4.57 /NA/0.12&quot; &quot;0.08/NA /3.90/NA /0.47/3.57 /0.00/0.04&quot; &quot;0.15/0.01 /3.58/0.72 /NA/1.80 /NA/0.00&quot; &quot;0.11/NA /4.55/NA /0.43/1.86 /0.00/0.00&quot; &quot;0.07/0.01 /3.14/0.73 /NA/3.40 /NA/0.03&quot; &quot;0.22/NA /4.96/NA /0.34/1.03 /0.00/NA&quot; &quot;0.30/0.03 /5.49/0.62 /NA/1.14 /NA/NA&quot; &quot;0.14/NA /5.81/NA /0.31/NA /NA/NA&quot; &quot;0.19/0.02 /5.42/0.36 /NA/NA /NA/NA&quot;"/>
775 </section> 954 </section>
776 <section name="tmt6plex"> 955 <section name="tmt6plex">
777 <param name="channel_126_description" value=""/> 956 <param name="channel_126_description" value=""/>
778 <param name="channel_127_description" value=""/> 957 <param name="channel_127_description" value=""/>
779 <param name="channel_128_description" value=""/> 958 <param name="channel_128_description" value=""/>
787 <output name="ctd_out" ftype="xml"> 966 <output name="ctd_out" ftype="xml">
788 <assert_contents> 967 <assert_contents>
789 <is_valid_xml/> 968 <is_valid_xml/>
790 </assert_contents> 969 </assert_contents>
791 </output> 970 </output>
971 <assert_stdout>
972 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
973 </assert_stdout>
792 </test> 974 </test>
793 </tests> 975 </tests>
794 <help><![CDATA[Calculates isobaric quantitative values for peptides 976 <help><![CDATA[Calculates isobaric quantitative values for peptides
795 977
796 978
797 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IsobaricAnalyzer.html]]></help> 979 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IsobaricAnalyzer.html]]></help>
798 <expand macro="references"/> 980 <expand macro="references"/>
799 </tool> 981 </tool>