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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 |
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<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Quantitation]--> <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Calculates isobaric quantitative values for peptides</description> <macros> <token name="@EXECUTABLE@">IsobaricAnalyzer</token> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ @EXT_FOO@ #import re ## Preprocessing mkdir in && ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call set -o pipefail && @EXECUTABLE@ -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && @EXECUTABLE@ -ini @EXECUTABLE@.ctd -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' -out 'out/output.${gxy2omsext("consensusxml")}' ## Postprocessing && mv 'out/output.${gxy2omsext("consensusxml")}' '$out' #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv '@EXECUTABLE@.ctd' '$ctd_out' #end if]]></command> <configfiles> <inputs name="args_json" data_style="paths"/> <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> <param argument="-type" type="select" optional="true" label="Isobaric Quantitation method used in the experiment" help=""> <option value="itraq4plex" selected="true">itraq4plex</option> <option value="itraq8plex">itraq8plex</option> <option value="tmt10plex">tmt10plex</option> <option value="tmt11plex">tmt11plex</option> <option value="tmt16plex">tmt16plex</option> <option value="tmt6plex">tmt6plex</option> <expand macro="list_string_san" name="type"/> </param> <param argument="-in" type="data" format="mzml" optional="false" label="input raw/picked data file" help=" select mzml data sets(s)"/> <section name="extraction" title="Parameters for the channel extraction" help="" expanded="false"> <param name="select_activation" argument="-extraction:select_activation" type="select" optional="true" label="Operate only on MSn scans where any of its precursors features a certain activation method" help="Setting to "auto" uses HCD and HCID spectra. Set to empty string if you want to disable filtering"> <option value="auto" selected="true">auto</option> <option value="Collision-induced dissociation">Collision-induced dissociation</option> <option value="Post-source decay">Post-source decay</option> <option value="Plasma desorption">Plasma desorption</option> <option value="Surface-induced dissociation">Surface-induced dissociation</option> <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> <option value="Electron capture dissociation">Electron capture dissociation</option> <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> <option value="Photodissociation">Photodissociation</option> <option value="Electron transfer dissociation">Electron transfer dissociation</option> <option value="Pulsed q dissociation">Pulsed q dissociation</option> <option value="trap-type collision-induced dissociation">trap-type collision-induced dissociation</option> <option value="beam-type collision-induced dissociation">beam-type collision-induced dissociation</option> <option value="in-source collision-induced dissociation">in-source collision-induced dissociation</option> <option value=""></option> <expand macro="list_string_san" name="select_activation"/> </param> <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=""/> <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"/> <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=""/> <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=""/> <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=""/> <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=""/> <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=""/> <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"/> </section> <section name="itraq4plex" title="Algorithm parameters for iTRAQ 4-plex" help="" expanded="false"> <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=""> <expand macro="list_string_san" name="channel_114_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_115_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_116_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_117_description"/> </param> <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=""/> <param name="correction_matrix" argument="-itraq4plex:correction_matrix" type="text" optional="true" value="0.0/1.0/5.9/0.2 0.0/2.0/5.6/0.1 0.0/3.0/4.5/0.1 0.1/4.0/3.5/0.1" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="correction_matrix"/> <expand macro="list_string_san" name="correction_matrix"/> </param> </section> <section name="itraq8plex" title="Algorithm parameters for iTRAQ 8-plex" help="" expanded="false"> <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=""> <expand macro="list_string_san" name="channel_113_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_114_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_115_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_116_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_117_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_118_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_119_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_121_description"/> </param> <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"/> <param name="correction_matrix" argument="-itraq8plex:correction_matrix" type="text" optional="true" value="0.00/0.00/6.89/0.22 0.00/0.94/5.90/0.16 0.00/1.88/4.90/0.10 0.00/2.82/3.90/0.07 0.06/3.77/2.99/0.00 0.09/4.71/1.88/0.00 0.14/5.66/0.87/0.00 0.27/7.44/0.18/0.00" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="correction_matrix"/> <expand macro="list_string_san" name="correction_matrix"/> </param> </section> <section name="quantification" title="Parameters for the peptide quantification" help="" expanded="false"> <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"/> <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!"/> </section> <section name="tmt10plex" title="Algorithm parameters for TMT 10-plex" help="" expanded="false"> <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=""> <expand macro="list_string_san" name="channel_126_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_127N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_127C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_128N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_128C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_129N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_129C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_130N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_130C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_131_description"/> </param> <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=""> <option value="126" selected="true">126</option> <option value="127N">127N</option> <option value="127C">127C</option> <option value="128N">128N</option> <option value="128C">128C</option> <option value="129N">129N</option> <option value="129C">129C</option> <option value="130N">130N</option> <option value="130C">130C</option> <option value="131">131</option> <expand macro="list_string_san" name="reference_channel"/> </param> <param name="correction_matrix" argument="-tmt10plex:correction_matrix" type="text" optional="true" value="0.0/0.0/5.09/0.0 0.0/0.25/5.27/0.0 0.0/0.37/5.36/0.15 0.0/0.65/4.17/0.1 0.08/0.49/3.06/0.0 0.01/0.71/3.07/0.0 0.0/1.32/2.62/0.0 0.02/1.28/2.75/2.53 0.03/2.08/2.23/0.0 0.08/1.99/1.65/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="correction_matrix"/> <expand macro="list_string_san" name="correction_matrix"/> </param> </section> <section name="tmt11plex" title="Algorithm parameters for TMT 11-plex" help="" expanded="false"> <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=""> <expand macro="list_string_san" name="channel_126_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_127N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_127C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_128N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_128C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_129N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_129C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_130N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_130C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_131N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_131C_description"/> </param> <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=""> <option value="126" selected="true">126</option> <option value="127N">127N</option> <option value="127C">127C</option> <option value="128N">128N</option> <option value="128C">128C</option> <option value="129N">129N</option> <option value="129C">129C</option> <option value="130N">130N</option> <option value="130C">130C</option> <option value="131N">131N</option> <option value="131C">131C</option> <expand macro="list_string_san" name="reference_channel"/> </param> <param name="correction_matrix" argument="-tmt11plex:correction_matrix" type="text" optional="true" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="correction_matrix"/> <expand macro="list_string_san" name="correction_matrix"/> </param> </section> <section name="tmt16plex" title="Algorithm parameters for TMT 16-plex" help="" expanded="false"> <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=""> <expand macro="list_string_san" name="channel_126_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_127N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_127C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_128N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_128C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_129N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_129C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_130N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_130C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_131N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_131C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_132N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_132C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_133N_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_133C_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_134N_description"/> </param> <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=""> <option value="126" selected="true">126</option> <option value="127N">127N</option> <option value="127C">127C</option> <option value="128N">128N</option> <option value="128C">128C</option> <option value="129N">129N</option> <option value="129C">129C</option> <option value="130N">130N</option> <option value="130C">130C</option> <option value="131N">131N</option> <option value="131C">131C</option> <option value="132N">132N</option> <option value="132C">132C</option> <option value="133N">133N</option> <option value="133C">133C</option> <option value="134N">134N</option> <expand macro="list_string_san" name="reference_channel"/> </param> <param name="correction_matrix" argument="-tmt16plex:correction_matrix" type="text" optional="true" value="0.0/0.0/8.02/0.0 0.0/0.68/7.46/0.0 0.0/0.71/6.94/0.0 0.0/1.88/6.67/0.0 0.0/1.34/5.59/0.0 0.0/2.41/5.48/0.0 0.0/2.34/5.19/0.0 0.0/3.53/4.57/0.0 0.0/2.67/4.16/0.0 0.0/3.92/3.73/0.0 0.0/3.69/3.14/0.0 0.0/3.22/2.76/0.0 0.0/4.11/2.0/0.0 0.0/3.85/1.58/0.0 0.0/4.63/1.18/0.0 0.0/5.22/0.86/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="correction_matrix"/> <expand macro="list_string_san" name="correction_matrix"/> </param> </section> <section name="tmt6plex" title="Algorithm parameters for TMT 6-plex" help="" expanded="false"> <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=""> <expand macro="list_string_san" name="channel_126_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_127_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_128_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_129_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_130_description"/> </param> <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=""> <expand macro="list_string_san" name="channel_131_description"/> </param> <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=""/> <param name="correction_matrix" argument="-tmt6plex:correction_matrix" type="text" optional="true" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="correction_matrix"/> <expand macro="list_string_san" name="correction_matrix"/> </param> </section> <expand macro="adv_opts_macro"> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> <outputs> <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> <tests><!-- TOPP_IsobaricAnalyzer_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="type" value="itraq4plex"/> <param name="in" value="IsobaricAnalyzer_input_1.mzML"/> <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="extraction"> <param name="select_activation"/> <param name="reporter_mass_shift" value="0.1"/> <param name="min_precursor_intensity" value="1.0"/> <param name="keep_unannotated_precursor" value="true"/> <param name="min_reporter_intensity" value="0.0"/> <param name="discard_low_intensity_quantifications" value="false"/> <param name="min_precursor_purity" value="0.0"/> <param name="precursor_isotope_deviation" value="10.0"/> <param name="purity_interpolation" value="true"/> </section> <section name="itraq4plex"> <param name="channel_114_description" value="l1"/> <param name="channel_115_description" value="l2"/> <param name="channel_116_description" value="l3"/> <param name="channel_117_description" value="lung"/> <param name="reference_channel" value="114"/> <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> </section> <section name="itraq8plex"> <param name="channel_113_description" value=""/> <param name="channel_114_description" value=""/> <param name="channel_115_description" value=""/> <param name="channel_116_description" value=""/> <param name="channel_117_description" value=""/> <param name="channel_118_description" value=""/> <param name="channel_119_description" value=""/> <param name="channel_121_description" value=""/> <param name="reference_channel" value="113"/> <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> </section> <section name="quantification"> <param name="isotope_correction" value="true"/> <param name="normalization" value="false"/> </section> <section name="tmt10plex"> <param name="channel_126_description" value=""/> <param name="channel_127N_description" value=""/> <param name="channel_127C_description" value=""/> <param name="channel_128N_description" value=""/> <param name="channel_128C_description" value=""/> <param name="channel_129N_description" value=""/> <param name="channel_129C_description" value=""/> <param name="channel_130N_description" value=""/> <param name="channel_130C_description" value=""/> <param name="channel_131_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> </section> <section name="tmt11plex"> <param name="channel_126_description" value=""/> <param name="channel_127N_description" value=""/> <param name="channel_127C_description" value=""/> <param name="channel_128N_description" value=""/> <param name="channel_128C_description" value=""/> <param name="channel_129N_description" value=""/> <param name="channel_129C_description" value=""/> <param name="channel_130N_description" value=""/> <param name="channel_130C_description" value=""/> <param name="channel_131N_description" value=""/> <param name="channel_131C_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> </section> <section name="tmt16plex"> <param name="channel_126_description" value=""/> <param name="channel_127N_description" value=""/> <param name="channel_127C_description" value=""/> <param name="channel_128N_description" value=""/> <param name="channel_128C_description" value=""/> <param name="channel_129N_description" value=""/> <param name="channel_129C_description" value=""/> <param name="channel_130N_description" value=""/> <param name="channel_130C_description" value=""/> <param name="channel_131N_description" value=""/> <param name="channel_131C_description" value=""/> <param name="channel_132N_description" value=""/> <param name="channel_132C_description" value=""/> <param name="channel_133N_description" value=""/> <param name="channel_133C_description" value=""/> <param name="channel_134N_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> </section> <section name="tmt6plex"> <param name="channel_126_description" value=""/> <param name="channel_127_description" value=""/> <param name="channel_128_description" value=""/> <param name="channel_129_description" value=""/> <param name="channel_130_description" value=""/> <param name="channel_131_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="type" value="itraq4plex"/> <param name="in" value="TMTTenPlexMethod_test.mzML"/> <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="extraction"> <param name="select_activation" value="auto"/> <param name="reporter_mass_shift" value="0.002"/> <param name="min_precursor_intensity" value="1.0"/> <param name="keep_unannotated_precursor" value="true"/> <param name="min_reporter_intensity" value="0.0"/> <param name="discard_low_intensity_quantifications" value="false"/> <param name="min_precursor_purity" value="0.0"/> <param name="precursor_isotope_deviation" value="10.0"/> <param name="purity_interpolation" value="true"/> </section> <section name="itraq4plex"> <param name="channel_114_description" value=""/> <param name="channel_115_description" value=""/> <param name="channel_116_description" value=""/> <param name="channel_117_description" value=""/> <param name="reference_channel" value="114"/> <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> </section> <section name="itraq8plex"> <param name="channel_113_description" value=""/> <param name="channel_114_description" value=""/> <param name="channel_115_description" value=""/> <param name="channel_116_description" value=""/> <param name="channel_117_description" value=""/> <param name="channel_118_description" value=""/> <param name="channel_119_description" value=""/> <param name="channel_121_description" value=""/> <param name="reference_channel" value="113"/> <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> </section> <section name="quantification"> <param name="isotope_correction" value="true"/> <param name="normalization" value="false"/> </section> <section name="tmt10plex"> <param name="channel_126_description" value=""/> <param name="channel_127N_description" value=""/> <param name="channel_127C_description" value=""/> <param name="channel_128N_description" value=""/> <param name="channel_128C_description" value=""/> <param name="channel_129N_description" value=""/> <param name="channel_129C_description" value=""/> <param name="channel_130N_description" value=""/> <param name="channel_130C_description" value=""/> <param name="channel_131_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/5.0/0.0" "0.0/0.2/4.6/0.0" "0.0/0.2/4.6/0.3" "0.0/0.9/4.7/0.2" "0.0/0.5/3.2/0.0" "0.0/0.7/3.3/0.0" "0.0/1.3/2.5/0.0" "0.0/1.2/2.8/2.7" "0.0/1.5/2.0/0.0" "0.0/1.5/1.9/0.0""/> </section> <section name="tmt11plex"> <param name="channel_126_description" value=""/> <param name="channel_127N_description" value=""/> <param name="channel_127C_description" value=""/> <param name="channel_128N_description" value=""/> <param name="channel_128C_description" value=""/> <param name="channel_129N_description" value=""/> <param name="channel_129C_description" value=""/> <param name="channel_130N_description" value=""/> <param name="channel_130C_description" value=""/> <param name="channel_131N_description" value=""/> <param name="channel_131C_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> </section> <section name="tmt16plex"> <param name="channel_126_description" value=""/> <param name="channel_127N_description" value=""/> <param name="channel_127C_description" value=""/> <param name="channel_128N_description" value=""/> <param name="channel_128C_description" value=""/> <param name="channel_129N_description" value=""/> <param name="channel_129C_description" value=""/> <param name="channel_130N_description" value=""/> <param name="channel_130C_description" value=""/> <param name="channel_131N_description" value=""/> <param name="channel_131C_description" value=""/> <param name="channel_132N_description" value=""/> <param name="channel_132C_description" value=""/> <param name="channel_133N_description" value=""/> <param name="channel_133C_description" value=""/> <param name="channel_134N_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> </section> <section name="tmt6plex"> <param name="channel_126_description" value=""/> <param name="channel_127_description" value=""/> <param name="channel_128_description" value=""/> <param name="channel_129_description" value=""/> <param name="channel_130_description" value=""/> <param name="channel_131_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="type" value="itraq4plex"/> <param name="in" value="TMTTenPlexMethod_test.mzML"/> <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="extraction"> <param name="select_activation" value="auto"/> <param name="reporter_mass_shift" value="0.002"/> <param name="min_precursor_intensity" value="1.0"/> <param name="keep_unannotated_precursor" value="true"/> <param name="min_reporter_intensity" value="0.0"/> <param name="discard_low_intensity_quantifications" value="false"/> <param name="min_precursor_purity" value="0.0"/> <param name="precursor_isotope_deviation" value="10.0"/> <param name="purity_interpolation" value="true"/> </section> <section name="itraq4plex"> <param name="channel_114_description" value=""/> <param name="channel_115_description" value=""/> <param name="channel_116_description" value=""/> <param name="channel_117_description" value=""/> <param name="reference_channel" value="114"/> <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> </section> <section name="itraq8plex"> <param name="channel_113_description" value=""/> <param name="channel_114_description" value=""/> <param name="channel_115_description" value=""/> <param name="channel_116_description" value=""/> <param name="channel_117_description" value=""/> <param name="channel_118_description" value=""/> <param name="channel_119_description" value=""/> <param name="channel_121_description" value=""/> <param name="reference_channel" value="113"/> <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> </section> <section name="quantification"> <param name="isotope_correction" value="true"/> <param name="normalization" value="false"/> </section> <section name="tmt10plex"> <param name="channel_126_description" value=""/> <param name="channel_127N_description" value=""/> <param name="channel_127C_description" value=""/> <param name="channel_128N_description" value=""/> <param name="channel_128C_description" value=""/> <param name="channel_129N_description" value=""/> <param name="channel_129C_description" value=""/> <param name="channel_130N_description" value=""/> <param name="channel_130C_description" value=""/> <param name="channel_131_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> </section> <section name="tmt11plex"> <param name="channel_126_description" value=""/> <param name="channel_127N_description" value=""/> <param name="channel_127C_description" value=""/> <param name="channel_128N_description" value=""/> <param name="channel_128C_description" value=""/> <param name="channel_129N_description" value=""/> <param name="channel_129C_description" value=""/> <param name="channel_130N_description" value=""/> <param name="channel_130C_description" value=""/> <param name="channel_131N_description" value=""/> <param name="channel_131C_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> </section> <section name="tmt16plex"> <param name="channel_126_description" value=""/> <param name="channel_127N_description" value=""/> <param name="channel_127C_description" value=""/> <param name="channel_128N_description" value=""/> <param name="channel_128C_description" value=""/> <param name="channel_129N_description" value=""/> <param name="channel_129C_description" value=""/> <param name="channel_130N_description" value=""/> <param name="channel_130C_description" value=""/> <param name="channel_131N_description" value=""/> <param name="channel_131C_description" value=""/> <param name="channel_132N_description" value=""/> <param name="channel_132C_description" value=""/> <param name="channel_133N_description" value=""/> <param name="channel_133C_description" value=""/> <param name="channel_134N_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> </section> <section name="tmt6plex"> <param name="channel_126_description" value=""/> <param name="channel_127_description" value=""/> <param name="channel_128_description" value=""/> <param name="channel_129_description" value=""/> <param name="channel_130_description" value=""/> <param name="channel_131_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_IsobaricAnalyzer_MS3TMT10Plex_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="type" value="tmt10plex"/> <param name="in" value="MS3_nonHierarchical.mzML"/> <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="extraction"> <param name="select_activation" value="Collision-induced dissociation"/> <param name="reporter_mass_shift" value="0.002"/> <param name="min_precursor_intensity" value="1.0"/> <param name="keep_unannotated_precursor" value="true"/> <param name="min_reporter_intensity" value="0.0"/> <param name="discard_low_intensity_quantifications" value="false"/> <param name="min_precursor_purity" value="0.0"/> <param name="precursor_isotope_deviation" value="10.0"/> <param name="purity_interpolation" value="true"/> </section> <section name="itraq4plex"> <param name="channel_114_description" value=""/> <param name="channel_115_description" value=""/> <param name="channel_116_description" value=""/> <param name="channel_117_description" value=""/> <param name="reference_channel" value="114"/> <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> </section> <section name="itraq8plex"> <param name="channel_113_description" value=""/> <param name="channel_114_description" value=""/> <param name="channel_115_description" value=""/> <param name="channel_116_description" value=""/> <param name="channel_117_description" value=""/> <param name="channel_118_description" value=""/> <param name="channel_119_description" value=""/> <param name="channel_121_description" value=""/> <param name="reference_channel" value="113"/> <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> </section> <section name="quantification"> <param name="isotope_correction" value="true"/> <param name="normalization" value="false"/> </section> <section name="tmt10plex"> <param name="channel_126_description" value=""/> <param name="channel_127N_description" value=""/> <param name="channel_127C_description" value=""/> <param name="channel_128N_description" value=""/> <param name="channel_128C_description" value=""/> <param name="channel_129N_description" value=""/> <param name="channel_129C_description" value=""/> <param name="channel_130N_description" value=""/> <param name="channel_130C_description" value=""/> <param name="channel_131_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/5.09/0.0" "0.0/0.25/5.27/0.0" "0.0/0.37/5.36/0.15" "0.0/0.65/4.17/0.1" "0.08/0.49/3.06/0.0" "0.01/0.71/3.07/0.0" "0.0/1.32/2.62/0.0" "0.02/1.28/2.75/2.53" "0.03/2.08/2.23/0.0" "0.08/1.99/1.65/0.0""/> </section> <section name="tmt11plex"> <param name="channel_126_description" value=""/> <param name="channel_127N_description" value=""/> <param name="channel_127C_description" value=""/> <param name="channel_128N_description" value=""/> <param name="channel_128C_description" value=""/> <param name="channel_129N_description" value=""/> <param name="channel_129C_description" value=""/> <param name="channel_130N_description" value=""/> <param name="channel_130C_description" value=""/> <param name="channel_131N_description" value=""/> <param name="channel_131C_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> </section> <section name="tmt16plex"> <param name="channel_126_description" value=""/> <param name="channel_127N_description" value=""/> <param name="channel_127C_description" value=""/> <param name="channel_128N_description" value=""/> <param name="channel_128C_description" value=""/> <param name="channel_129N_description" value=""/> <param name="channel_129C_description" value=""/> <param name="channel_130N_description" value=""/> <param name="channel_130C_description" value=""/> <param name="channel_131N_description" value=""/> <param name="channel_131C_description" value=""/> <param name="channel_132N_description" value=""/> <param name="channel_132C_description" value=""/> <param name="channel_133N_description" value=""/> <param name="channel_133C_description" value=""/> <param name="channel_134N_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> </section> <section name="tmt6plex"> <param name="channel_126_description" value=""/> <param name="channel_127_description" value=""/> <param name="channel_128_description" value=""/> <param name="channel_129_description" value=""/> <param name="channel_130_description" value=""/> <param name="channel_131_description" value=""/> <param name="reference_channel" value="126"/> <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> </tests> <help><![CDATA[Calculates isobaric quantitative values for peptides For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IsobaricAnalyzer.html]]></help> <expand macro="references"/> </tool>