Mercurial > repos > galaxyp > openms_isobaricanalyzer
diff IsobaricAnalyzer.xml @ 14:30f67afbf5be draft default tip
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 |
| children |
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--- a/IsobaricAnalyzer.xml Thu Dec 01 19:12:40 2022 +0000 +++ b/IsobaricAnalyzer.xml Fri Jun 14 21:32:32 2024 +0000 @@ -1,4 +1,3 @@ -<?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"> @@ -15,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call @@ -39,18 +38,19 @@ <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=""> + <param argument="-type" type="select" 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="tmt18plex">tmt18plex</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)"/> + <param argument="-in" type="data" format="mzml" 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"> + <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 "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> @@ -68,16 +68,16 @@ <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> + <option value="any">any</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="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=""/> + <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"/> <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="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=""/> <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="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=""/> + <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=""/> <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"> @@ -93,8 +93,8 @@ <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)"> + <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=""/> + <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: <-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> @@ -124,8 +124,8 @@ <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)"> + <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"/> + <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: <-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> @@ -165,7 +165,7 @@ <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=""> + <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=""> <option value="126" selected="true">126</option> <option value="127N">127N</option> <option value="127C">127C</option> @@ -178,7 +178,7 @@ <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)"> + <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: <-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> @@ -217,7 +217,7 @@ <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=""> + <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=""> <option value="126" selected="true">126</option> <option value="127N">127N</option> <option value="127C">127C</option> @@ -231,7 +231,7 @@ <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)"> + <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: <-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> @@ -285,7 +285,7 @@ <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=""> + <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=""> <option value="126" selected="true">126</option> <option value="127N">127N</option> <option value="127C">127C</option> @@ -304,7 +304,88 @@ <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)"> + <param name="correction_matrix" argument="-tmt16plex:correction_matrix" type="text" value=""NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32" "NA/NA / NA/0.78 / NA/9.41 / NA/0.33" "NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27" "NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26" "0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15" "0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15" "0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09" "0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10" "0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06" "0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12" "0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04" "0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00" "0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00" "0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03" "0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA" "0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA"" 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: <-2C13>/<-N15-C13>/<-C13>/<-N15>/<+N15>/<+C13>/<+N15+C13>/<+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)"> + <expand macro="list_string_val" name="correction_matrix"/> + <expand macro="list_string_san" name="correction_matrix"/> + </param> + </section> + <section name="tmt18plex" title="Algorithm parameters for TMT 18-plex" help="" expanded="false"> + <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=""> + <expand macro="list_string_san" name="channel_126_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_127N_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_127C_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_128N_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_128C_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_129N_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_129C_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_130N_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_130C_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_131N_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_131C_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_132N_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_132C_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_133N_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_133C_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_134N_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_134C_description"/> + </param> + <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=""> + <expand macro="list_string_san" name="channel_135N_description"/> + </param> + <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=""> + <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> + <option value="134C">134C</option> + <option value="135N">135N</option> + <expand macro="list_string_san" name="reference_channel"/> + </param> + <param name="correction_matrix" argument="-tmt18plex:correction_matrix" type="text" value=""NA/NA /NA/NA /0.31/9.09 /0.02/0.32" "NA/NA /NA/0.78 /NA/9.41 /NA/0.33" "NA/NA /0.93/NA /0.35/8.63 /0.01/0.27" "NA/0.00 /0.82/0.65 /NA/8.13 /NA/0.26" "0.00/NA /1.47/NA /0.34/6.91 /0.00/0.15" "0.00/0.00 /1.46/1.28 /NA/6.86 /NA/0.15" "0.13/NA /2.59/NA /0.32/6.07 /0.1/0.09" "0.13/0.00 /2.41/0.27 /NA/5.58 /NA/0.10" "0.04/NA /3.10/NA /0.42/4.82 /0.02/0.06" "0.03/0.00 /2.78/0.63 /NA/4.57 /NA/0.12" "0.08/NA /3.90/NA /0.47/3.57 /0.00/0.04" "0.15/0.01 /3.58/0.72 /NA/1.80 /NA/0.00" "0.11/NA /4.55/NA /0.43/1.86 /0.00/0.00" "0.07/0.01 /3.14/0.73 /NA/3.40 /NA/0.03" "0.22/NA /4.96/NA /0.34/1.03 /0.00/NA" "0.30/0.03 /5.49/0.62 /NA/1.14 /NA/NA" "0.14/NA /5.81/NA /0.31/NA /NA/NA" "0.19/0.02 /5.42/0.36 /NA/NA /NA/NA"" 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: <-2C13>/<-N15-C13>/<-C13>/<-N15>/<+N15>/<+C13>/<+N15+C13>/<+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)"> <expand macro="list_string_val" name="correction_matrix"/> <expand macro="list_string_san" name="correction_matrix"/> </param> @@ -328,15 +409,15 @@ <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)"> + <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=""/> + <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: <-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=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -350,7 +431,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_IsobaricAnalyzer_1 --> + <tests> + <!-- TOPP_IsobaricAnalyzer_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> @@ -358,9 +440,9 @@ </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"/> + <output name="out" value="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="extraction"> - <param name="select_activation"/> + <param name="select_activation" value="any"/> <param name="reporter_mass_shift" value="0.1"/> <param name="min_precursor_intensity" value="1.0"/> <param name="keep_unannotated_precursor" value="true"/> @@ -441,7 +523,29 @@ <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""/> + <param name="correction_matrix" value=""NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32" "NA/NA / NA/0.78 / NA/9.41 / NA/0.33" "NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27" "NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26" "0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15" "0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15" "0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09" "0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10" "0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06" "0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12" "0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04" "0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00" "0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00" "0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03" "0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA" "0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA""/> + </section> + <section name="tmt18plex"> + <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="channel_134C_description" value=""/> + <param name="channel_135N_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""NA/NA /NA/NA /0.31/9.09 /0.02/0.32" "NA/NA /NA/0.78 /NA/9.41 /NA/0.33" "NA/NA /0.93/NA /0.35/8.63 /0.01/0.27" "NA/0.00 /0.82/0.65 /NA/8.13 /NA/0.26" "0.00/NA /1.47/NA /0.34/6.91 /0.00/0.15" "0.00/0.00 /1.46/1.28 /NA/6.86 /NA/0.15" "0.13/NA /2.59/NA /0.32/6.07 /0.1/0.09" "0.13/0.00 /2.41/0.27 /NA/5.58 /NA/0.10" "0.04/NA /3.10/NA /0.42/4.82 /0.02/0.06" "0.03/0.00 /2.78/0.63 /NA/4.57 /NA/0.12" "0.08/NA /3.90/NA /0.47/3.57 /0.00/0.04" "0.15/0.01 /3.58/0.72 /NA/1.80 /NA/0.00" "0.11/NA /4.55/NA /0.43/1.86 /0.00/0.00" "0.07/0.01 /3.14/0.73 /NA/3.40 /NA/0.03" "0.22/NA /4.96/NA /0.34/1.03 /0.00/NA" "0.30/0.03 /5.49/0.62 /NA/1.14 /NA/NA" "0.14/NA /5.81/NA /0.31/NA /NA/NA" "0.19/0.02 /5.42/0.36 /NA/NA /NA/NA""/> </section> <section name="tmt6plex"> <param name="channel_126_description" value=""/> @@ -459,6 +563,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1 --> <test expect_num_outputs="2"> @@ -468,7 +575,7 @@ </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"/> + <output name="out" value="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"/> @@ -551,7 +658,29 @@ <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""/> + <param name="correction_matrix" value=""NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32" "NA/NA / NA/0.78 / NA/9.41 / NA/0.33" "NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27" "NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26" "0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15" "0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15" "0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09" "0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10" "0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06" "0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12" "0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04" "0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00" "0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00" "0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03" "0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA" "0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA""/> + </section> + <section name="tmt18plex"> + <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="channel_134C_description" value=""/> + <param name="channel_135N_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""NA/NA /NA/NA /0.31/9.09 /0.02/0.32" "NA/NA /NA/0.78 /NA/9.41 /NA/0.33" "NA/NA /0.93/NA /0.35/8.63 /0.01/0.27" "NA/0.00 /0.82/0.65 /NA/8.13 /NA/0.26" "0.00/NA /1.47/NA /0.34/6.91 /0.00/0.15" "0.00/0.00 /1.46/1.28 /NA/6.86 /NA/0.15" "0.13/NA /2.59/NA /0.32/6.07 /0.1/0.09" "0.13/0.00 /2.41/0.27 /NA/5.58 /NA/0.10" "0.04/NA /3.10/NA /0.42/4.82 /0.02/0.06" "0.03/0.00 /2.78/0.63 /NA/4.57 /NA/0.12" "0.08/NA /3.90/NA /0.47/3.57 /0.00/0.04" "0.15/0.01 /3.58/0.72 /NA/1.80 /NA/0.00" "0.11/NA /4.55/NA /0.43/1.86 /0.00/0.00" "0.07/0.01 /3.14/0.73 /NA/3.40 /NA/0.03" "0.22/NA /4.96/NA /0.34/1.03 /0.00/NA" "0.30/0.03 /5.49/0.62 /NA/1.14 /NA/NA" "0.14/NA /5.81/NA /0.31/NA /NA/NA" "0.19/0.02 /5.42/0.36 /NA/NA /NA/NA""/> </section> <section name="tmt6plex"> <param name="channel_126_description" value=""/> @@ -569,6 +698,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1 --> <test expect_num_outputs="2"> @@ -578,7 +710,7 @@ </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"/> + <output name="out" value="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"/> @@ -661,7 +793,29 @@ <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""/> + <param name="correction_matrix" value=""NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32" "NA/NA / NA/0.78 / NA/9.41 / NA/0.33" "NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27" "NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26" "0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15" "0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15" "0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09" "0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10" "0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06" "0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12" "0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04" "0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00" "0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00" "0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03" "0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA" "0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA""/> + </section> + <section name="tmt18plex"> + <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="channel_134C_description" value=""/> + <param name="channel_135N_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""NA/NA /NA/NA /0.31/9.09 /0.02/0.32" "NA/NA /NA/0.78 /NA/9.41 /NA/0.33" "NA/NA /0.93/NA /0.35/8.63 /0.01/0.27" "NA/0.00 /0.82/0.65 /NA/8.13 /NA/0.26" "0.00/NA /1.47/NA /0.34/6.91 /0.00/0.15" "0.00/0.00 /1.46/1.28 /NA/6.86 /NA/0.15" "0.13/NA /2.59/NA /0.32/6.07 /0.1/0.09" "0.13/0.00 /2.41/0.27 /NA/5.58 /NA/0.10" "0.04/NA /3.10/NA /0.42/4.82 /0.02/0.06" "0.03/0.00 /2.78/0.63 /NA/4.57 /NA/0.12" "0.08/NA /3.90/NA /0.47/3.57 /0.00/0.04" "0.15/0.01 /3.58/0.72 /NA/1.80 /NA/0.00" "0.11/NA /4.55/NA /0.43/1.86 /0.00/0.00" "0.07/0.01 /3.14/0.73 /NA/3.40 /NA/0.03" "0.22/NA /4.96/NA /0.34/1.03 /0.00/NA" "0.30/0.03 /5.49/0.62 /NA/1.14 /NA/NA" "0.14/NA /5.81/NA /0.31/NA /NA/NA" "0.19/0.02 /5.42/0.36 /NA/NA /NA/NA""/> </section> <section name="tmt6plex"> <param name="channel_126_description" value=""/> @@ -679,6 +833,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_IsobaricAnalyzer_MS3TMT10Plex_1 --> <test expect_num_outputs="2"> @@ -688,7 +845,7 @@ </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"/> + <output name="out" value="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"/> @@ -771,7 +928,29 @@ <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""/> + <param name="correction_matrix" value=""NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32" "NA/NA / NA/0.78 / NA/9.41 / NA/0.33" "NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27" "NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26" "0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15" "0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15" "0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09" "0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10" "0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06" "0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12" "0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04" "0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00" "0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00" "0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03" "0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA" "0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA""/> + </section> + <section name="tmt18plex"> + <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="channel_134C_description" value=""/> + <param name="channel_135N_description" value=""/> + <param name="reference_channel" value="126"/> + <param name="correction_matrix" value=""NA/NA /NA/NA /0.31/9.09 /0.02/0.32" "NA/NA /NA/0.78 /NA/9.41 /NA/0.33" "NA/NA /0.93/NA /0.35/8.63 /0.01/0.27" "NA/0.00 /0.82/0.65 /NA/8.13 /NA/0.26" "0.00/NA /1.47/NA /0.34/6.91 /0.00/0.15" "0.00/0.00 /1.46/1.28 /NA/6.86 /NA/0.15" "0.13/NA /2.59/NA /0.32/6.07 /0.1/0.09" "0.13/0.00 /2.41/0.27 /NA/5.58 /NA/0.10" "0.04/NA /3.10/NA /0.42/4.82 /0.02/0.06" "0.03/0.00 /2.78/0.63 /NA/4.57 /NA/0.12" "0.08/NA /3.90/NA /0.47/3.57 /0.00/0.04" "0.15/0.01 /3.58/0.72 /NA/1.80 /NA/0.00" "0.11/NA /4.55/NA /0.43/1.86 /0.00/0.00" "0.07/0.01 /3.14/0.73 /NA/3.40 /NA/0.03" "0.22/NA /4.96/NA /0.34/1.03 /0.00/NA" "0.30/0.03 /5.49/0.62 /NA/1.14 /NA/NA" "0.14/NA /5.81/NA /0.31/NA /NA/NA" "0.19/0.02 /5.42/0.36 /NA/NA /NA/NA""/> </section> <section name="tmt6plex"> <param name="channel_126_description" value=""/> @@ -789,11 +968,14 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </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> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IsobaricAnalyzer.html]]></help> <expand macro="references"/> </tool>