Mercurial > repos > galaxyp > openms_isobaricanalyzer
diff IsobaricAnalyzer.xml @ 9:d52e76ea2c11 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
---|---|
date | Wed, 09 Sep 2020 12:52:01 +0000 |
parents | 7d2ed325f2e5 |
children | 57a06b90bb00 |
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--- a/IsobaricAnalyzer.xml Fri May 17 09:20:14 2019 -0400 +++ b/IsobaricAnalyzer.xml Wed Sep 09 12:52:01 2020 +0000 @@ -1,740 +1,359 @@ <?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="2.3.0"> +<tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Calculates isobaric quantitative values for peptides</description> <macros> <token name="@EXECUTABLE@">IsobaricAnalyzer</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[IsobaricAnalyzer + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $param_type: - -type - #if " " in str($param_type): - "$param_type" - #else - $param_type - #end if -#end if -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_id_pool: - -id_pool "$param_id_pool" -#end if -#if $param_extraction_select_activation: - -extraction:select_activation - #if " " in str($param_extraction_select_activation): - "$param_extraction_select_activation" - #else - $param_extraction_select_activation - #end if -#end if -#if $param_extraction_reporter_mass_shift: - -extraction:reporter_mass_shift $param_extraction_reporter_mass_shift -#end if -#if $param_extraction_min_precursor_intensity: - -extraction:min_precursor_intensity $param_extraction_min_precursor_intensity -#end if -#if $param_extraction_keep_unannotated_precursor: - -extraction:keep_unannotated_precursor - #if " " in str($param_extraction_keep_unannotated_precursor): - "$param_extraction_keep_unannotated_precursor" - #else - $param_extraction_keep_unannotated_precursor - #end if -#end if -#if $param_extraction_min_reporter_intensity: - -extraction:min_reporter_intensity $param_extraction_min_reporter_intensity -#end if -#if $param_extraction_discard_low_intensity_quantifications: - -extraction:discard_low_intensity_quantifications -#end if -#if $param_extraction_min_precursor_purity: - -extraction:min_precursor_purity $param_extraction_min_precursor_purity -#end if -#if $param_itraq4plex_channel_114_description: - -itraq4plex:channel_114_description "$param_itraq4plex_channel_114_description" -#end if -#if $param_itraq4plex_channel_115_description: - -itraq4plex:channel_115_description "$param_itraq4plex_channel_115_description" -#end if -#if $param_itraq4plex_channel_116_description: - -itraq4plex:channel_116_description "$param_itraq4plex_channel_116_description" -#end if -#if $param_itraq4plex_channel_117_description: - -itraq4plex:channel_117_description "$param_itraq4plex_channel_117_description" -#end if -#if $param_itraq4plex_reference_channel: - -itraq4plex:reference_channel $param_itraq4plex_reference_channel -#end if +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +mkdir out && -#if $rep_param_itraq4plex_correction_matrix: --itraq4plex:correction_matrix - #for token in $rep_param_itraq4plex_correction_matrix: - #if " " in str(token): - "$token.param_itraq4plex_correction_matrix" - #else - $token.param_itraq4plex_correction_matrix - #end if - #end for -#end if -#if $param_itraq8plex_channel_113_description: - -itraq8plex:channel_113_description "$param_itraq8plex_channel_113_description" -#end if -#if $param_itraq8plex_channel_114_description: - -itraq8plex:channel_114_description "$param_itraq8plex_channel_114_description" -#end if -#if $param_itraq8plex_channel_115_description: - -itraq8plex:channel_115_description "$param_itraq8plex_channel_115_description" -#end if -#if $param_itraq8plex_channel_116_description: - -itraq8plex:channel_116_description "$param_itraq8plex_channel_116_description" -#end if -#if $param_itraq8plex_channel_117_description: - -itraq8plex:channel_117_description "$param_itraq8plex_channel_117_description" -#end if -#if $param_itraq8plex_channel_118_description: - -itraq8plex:channel_118_description "$param_itraq8plex_channel_118_description" -#end if -#if $param_itraq8plex_channel_119_description: - -itraq8plex:channel_119_description "$param_itraq8plex_channel_119_description" -#end if -#if $param_itraq8plex_channel_121_description: - -itraq8plex:channel_121_description "$param_itraq8plex_channel_121_description" -#end if -#if $param_itraq8plex_reference_channel: - -itraq8plex:reference_channel $param_itraq8plex_reference_channel -#end if +## Main program call -#if $rep_param_itraq8plex_correction_matrix: --itraq8plex:correction_matrix - #for token in $rep_param_itraq8plex_correction_matrix: - #if " " in str(token): - "$token.param_itraq8plex_correction_matrix" - #else - $token.param_itraq8plex_correction_matrix - #end if - #end for -#end if -#if $param_quantification_isotope_correction: - -quantification:isotope_correction - #if " " in str($param_quantification_isotope_correction): - "$param_quantification_isotope_correction" - #else - $param_quantification_isotope_correction - #end if -#end if -#if $param_quantification_normalization: - -quantification:normalization -#end if -#if $param_tmt10plex_channel_126_description: - -tmt10plex:channel_126_description "$param_tmt10plex_channel_126_description" -#end if -#if $param_tmt10plex_channel_127N_description: - -tmt10plex:channel_127N_description "$param_tmt10plex_channel_127N_description" -#end if -#if $param_tmt10plex_channel_127C_description: - -tmt10plex:channel_127C_description "$param_tmt10plex_channel_127C_description" -#end if -#if $param_tmt10plex_channel_128N_description: - -tmt10plex:channel_128N_description "$param_tmt10plex_channel_128N_description" -#end if -#if $param_tmt10plex_channel_128C_description: - -tmt10plex:channel_128C_description "$param_tmt10plex_channel_128C_description" -#end if -#if $param_tmt10plex_channel_129N_description: - -tmt10plex:channel_129N_description "$param_tmt10plex_channel_129N_description" -#end if -#if $param_tmt10plex_channel_129C_description: - -tmt10plex:channel_129C_description "$param_tmt10plex_channel_129C_description" -#end if -#if $param_tmt10plex_channel_130N_description: - -tmt10plex:channel_130N_description "$param_tmt10plex_channel_130N_description" -#end if -#if $param_tmt10plex_channel_130C_description: - -tmt10plex:channel_130C_description "$param_tmt10plex_channel_130C_description" -#end if -#if $param_tmt10plex_channel_131_description: - -tmt10plex:channel_131_description "$param_tmt10plex_channel_131_description" -#end if -#if $param_tmt10plex_reference_channel: - -tmt10plex:reference_channel - #if " " in str($param_tmt10plex_reference_channel): - "$param_tmt10plex_reference_channel" - #else - $param_tmt10plex_reference_channel - #end if -#end if +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__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")}' -#if $rep_param_tmt10plex_correction_matrix: --tmt10plex:correction_matrix - #for token in $rep_param_tmt10plex_correction_matrix: - #if " " in str(token): - "$token.param_tmt10plex_correction_matrix" - #else - $token.param_tmt10plex_correction_matrix - #end if - #end for -#end if -#if $param_tmt11plex_channel_126_description: - -tmt11plex:channel_126_description "$param_tmt11plex_channel_126_description" -#end if -#if $param_tmt11plex_channel_127N_description: - -tmt11plex:channel_127N_description "$param_tmt11plex_channel_127N_description" -#end if -#if $param_tmt11plex_channel_127C_description: - -tmt11plex:channel_127C_description "$param_tmt11plex_channel_127C_description" -#end if -#if $param_tmt11plex_channel_128N_description: - -tmt11plex:channel_128N_description "$param_tmt11plex_channel_128N_description" -#end if -#if $param_tmt11plex_channel_128C_description: - -tmt11plex:channel_128C_description "$param_tmt11plex_channel_128C_description" -#end if -#if $param_tmt11plex_channel_129N_description: - -tmt11plex:channel_129N_description "$param_tmt11plex_channel_129N_description" -#end if -#if $param_tmt11plex_channel_129C_description: - -tmt11plex:channel_129C_description "$param_tmt11plex_channel_129C_description" -#end if -#if $param_tmt11plex_channel_130N_description: - -tmt11plex:channel_130N_description "$param_tmt11plex_channel_130N_description" -#end if -#if $param_tmt11plex_channel_130C_description: - -tmt11plex:channel_130C_description "$param_tmt11plex_channel_130C_description" -#end if -#if $param_tmt11plex_channel_131N_description: - -tmt11plex:channel_131N_description "$param_tmt11plex_channel_131N_description" -#end if -#if $param_tmt11plex_channel_131C_description: - -tmt11plex:channel_131C_description "$param_tmt11plex_channel_131C_description" -#end if -#if $param_tmt11plex_reference_channel: - -tmt11plex:reference_channel - #if " " in str($param_tmt11plex_reference_channel): - "$param_tmt11plex_reference_channel" - #else - $param_tmt11plex_reference_channel - #end if -#end if - -#if $rep_param_tmt11plex_correction_matrix: --tmt11plex:correction_matrix - #for token in $rep_param_tmt11plex_correction_matrix: - #if " " in str(token): - "$token.param_tmt11plex_correction_matrix" - #else - $token.param_tmt11plex_correction_matrix - #end if - #end for -#end if -#if $param_tmt6plex_channel_126_description: - -tmt6plex:channel_126_description "$param_tmt6plex_channel_126_description" -#end if -#if $param_tmt6plex_channel_127_description: - -tmt6plex:channel_127_description "$param_tmt6plex_channel_127_description" -#end if -#if $param_tmt6plex_channel_128_description: - -tmt6plex:channel_128_description "$param_tmt6plex_channel_128_description" -#end if -#if $param_tmt6plex_channel_129_description: - -tmt6plex:channel_129_description "$param_tmt6plex_channel_129_description" -#end if -#if $param_tmt6plex_channel_130_description: - -tmt6plex:channel_130_description "$param_tmt6plex_channel_130_description" -#end if -#if $param_tmt6plex_channel_131_description: - -tmt6plex:channel_131_description "$param_tmt6plex_channel_131_description" -#end if -#if $param_tmt6plex_reference_channel: - -tmt6plex:reference_channel $param_tmt6plex_reference_channel -#end if - -#if $rep_param_tmt6plex_correction_matrix: --tmt6plex:correction_matrix - #for token in $rep_param_tmt6plex_correction_matrix: - #if " " in str(token): - "$token.param_tmt6plex_correction_matrix" - #else - $token.param_tmt6plex_correction_matrix - #end if - #end for -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if - #if $adv_opts.param_extraction_precursor_isotope_deviation: - -extraction:precursor_isotope_deviation $adv_opts.param_extraction_precursor_isotope_deviation -#end if - #if $adv_opts.param_extraction_purity_interpolation: - -extraction:purity_interpolation - #if " " in str($adv_opts.param_extraction_purity_interpolation): - "$adv_opts.param_extraction_purity_interpolation" - #else - $adv_opts.param_extraction_purity_interpolation - #end if -#end if -#end if -]]></command> +## Postprocessing +&& mv 'out/output.${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 name="param_type" type="select" optional="False" value="itraq4plex" label="Isobaric Quantitation method used in the experiment" help="(-type) "> + <param name="type" argument="-type" type="select" optional="false" 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> - </param> - <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/> - <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use share/OpenMS/IDPool/IDPool.txt)"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_extraction_select_activation" type="select" optional="False" value="High-energy collision-induced dissociation" label="Operate only on MSn scans where any of its precursors features a certain activation method (" help="(-select_activation) e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering"> - <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" selected="true">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=""></option> - </param> - <param name="param_extraction_reporter_mass_shift" type="float" min="0.0001" max="0.5" optional="True" value="0.002" label="Allowed shift (left to right) in Th from the expected position" help="(-reporter_mass_shift) "/> - <param name="param_extraction_min_precursor_intensity" type="float" min="0.0" optional="True" value="1.0" label="Minimum intensity of the precursor to be extracted" help="(-min_precursor_intensity) MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/> - <param name="param_extraction_keep_unannotated_precursor" display="radio" type="select" optional="False" value="true" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help="(-keep_unannotated_precursor) "> - <option value="true" selected="true">true</option> - <option value="false">false</option> - </param> - <param name="param_extraction_min_reporter_intensity" type="float" min="0.0" optional="True" value="0.0" label="Minimum intensity of the individual reporter ions to be extracted" help="(-min_reporter_intensity) "/> - <param name="param_extraction_discard_low_intensity_quantifications" display="radio" type="boolean" truevalue="-extraction:discard_low_intensity_quantifications" falsevalue="" checked="false" optional="True" label="Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'" help="(-discard_low_intensity_quantifications) "/> - <param name="param_extraction_min_precursor_purity" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precurso" help="(-min_precursor_purity) "/> - <param name="param_itraq4plex_channel_114_description" type="text" size="30" label="Description for the content of the 114 channel" help="(-channel_114_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_itraq4plex_channel_115_description" type="text" size="30" label="Description for the content of the 115 channel" help="(-channel_115_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_itraq4plex_channel_116_description" type="text" size="30" label="Description for the content of the 116 channel" help="(-channel_116_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_itraq4plex_channel_117_description" type="text" size="30" label="Description for the content of the 117 channel" help="(-channel_117_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_itraq4plex_reference_channel" type="integer" min="114" max="117" optional="True" value="114" label="Number of the reference channel (114-117)" help="(-reference_channel) "/> - <repeat name="rep_param_itraq4plex_correction_matrix" min="0" max="1" title="param_itraq4plex_correction_matrix"> - <param name="param_itraq4plex_correction_matrix" type="text" size="30" 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="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - </repeat> - <param name="param_itraq8plex_channel_113_description" type="text" size="30" label="Description for the content of the 113 channel" help="(-channel_113_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_itraq8plex_channel_114_description" type="text" size="30" label="Description for the content of the 114 channel" help="(-channel_114_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_itraq8plex_channel_115_description" type="text" size="30" label="Description for the content of the 115 channel" help="(-channel_115_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_itraq8plex_channel_116_description" type="text" size="30" label="Description for the content of the 116 channel" help="(-channel_116_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_itraq8plex_channel_117_description" type="text" size="30" label="Description for the content of the 117 channel" help="(-channel_117_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_itraq8plex_channel_118_description" type="text" size="30" label="Description for the content of the 118 channel" help="(-channel_118_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_itraq8plex_channel_119_description" type="text" size="30" label="Description for the content of the 119 channel" help="(-channel_119_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_itraq8plex_channel_121_description" type="text" size="30" label="Description for the content of the 121 channel" help="(-channel_121_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_itraq8plex_reference_channel" type="integer" min="113" max="121" optional="True" value="113" label="Number of the reference channel (113-121)" help="(-reference_channel) Please note that 120 is not valid"/> - <repeat name="rep_param_itraq8plex_correction_matrix" min="0" max="1" title="param_itraq8plex_correction_matrix"> - <param name="param_itraq8plex_correction_matrix" type="text" size="30" 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="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - </repeat> - <param name="param_quantification_isotope_correction" display="radio" type="select" optional="False" value="true" label="Enable isotope correction (highly recommended)" help="(-isotope_correction) Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results"> - <option value="true" selected="true">true</option> - <option value="false">false</option> - </param> - <param name="param_quantification_normalization" display="radio" type="boolean" truevalue="-quantification:normalization" falsevalue="" checked="false" optional="True" label="Enable normalization of channel intensities with respect to the reference channel" help="(-normalization) 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!"/> - <param name="param_tmt10plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt10plex_channel_127N_description" type="text" size="30" label="Description for the content of the 127N channel" help="(-channel_127N_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt10plex_channel_127C_description" type="text" size="30" label="Description for the content of the 127C channel" help="(-channel_127C_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt10plex_channel_128N_description" type="text" size="30" label="Description for the content of the 128N channel" help="(-channel_128N_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt10plex_channel_128C_description" type="text" size="30" label="Description for the content of the 128C channel" help="(-channel_128C_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt10plex_channel_129N_description" type="text" size="30" label="Description for the content of the 129N channel" help="(-channel_129N_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt10plex_channel_129C_description" type="text" size="30" label="Description for the content of the 129C channel" help="(-channel_129C_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <expand macro="list_string_san"/> </param> - <param name="param_tmt10plex_channel_130N_description" type="text" size="30" label="Description for the content of the 130N channel" help="(-channel_130N_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt10plex_channel_130C_description" type="text" size="30" label="Description for the content of the 130C channel" help="(-channel_130C_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt10plex_channel_131_description" type="text" size="30" label="Description for the content of the 131 channel" help="(-channel_131_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt10plex_reference_channel" type="select" optional="False" value="126" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" help="(-reference_channel) "> - <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> - </param> - <repeat name="rep_param_tmt10plex_correction_matrix" min="0" max="1" title="param_tmt10plex_correction_matrix"> - <param name="param_tmt10plex_correction_matrix" type="text" size="30" 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" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="in" 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="false" label="Operate only on MSn scans where any of its precursors features a certain activation method" help="(e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering"> + <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" selected="true">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=""></option> + <expand macro="list_string_san"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + <expand macro="list_string_san"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + <expand macro="list_string_san"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </param> + <param name="reference_channel" argument="-tmt10plex:reference_channel" type="select" optional="false" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" help=""> + <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"/> + </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"/> + <expand macro="list_string_san"/> + </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"/> + </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"/> + </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"/> + </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"/> </param> - </repeat> - <param name="param_tmt11plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt11plex_channel_127N_description" type="text" size="30" label="Description for the content of the 127N channel" help="(-channel_127N_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt11plex_channel_127C_description" type="text" size="30" label="Description for the content of the 127C channel" help="(-channel_127C_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt11plex_channel_128N_description" type="text" size="30" label="Description for the content of the 128N channel" help="(-channel_128N_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt11plex_channel_128C_description" type="text" size="30" label="Description for the content of the 128C channel" help="(-channel_128C_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt11plex_channel_129N_description" type="text" size="30" label="Description for the content of the 129N channel" help="(-channel_129N_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt11plex_channel_129C_description" type="text" size="30" label="Description for the content of the 129C channel" help="(-channel_129C_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt11plex_channel_130N_description" type="text" size="30" label="Description for the content of the 130N channel" help="(-channel_130N_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt11plex_channel_130C_description" type="text" size="30" label="Description for the content of the 130C channel" help="(-channel_130C_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt11plex_channel_131N_description" type="text" size="30" label="Description for the content of the 131N channel" help="(-channel_131N_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt11plex_channel_131C_description" type="text" size="30" label="Description for the content of the 131C channel" help="(-channel_131C_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt11plex_reference_channel" type="select" optional="False" value="126" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help="(-reference_channel) "> - <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> - </param> - <repeat name="rep_param_tmt11plex_correction_matrix" min="0" max="1" title="param_tmt11plex_correction_matrix"> - <param name="param_tmt11plex_correction_matrix" type="text" size="30" 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="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </param> + <param name="reference_channel" argument="-tmt11plex:reference_channel" type="select" optional="false" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help=""> + <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"/> + </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"/> + <expand macro="list_string_san"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> </param> - </repeat> - <param name="param_tmt6plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt6plex_channel_127_description" type="text" size="30" label="Description for the content of the 127 channel" help="(-channel_127_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt6plex_channel_128_description" type="text" size="30" label="Description for the content of the 128 channel" help="(-channel_128_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt6plex_channel_129_description" type="text" size="30" label="Description for the content of the 129 channel" help="(-channel_129_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt6plex_channel_130_description" type="text" size="30" label="Description for the content of the 130 channel" help="(-channel_130_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt6plex_channel_131_description" type="text" size="30" label="Description for the content of the 131 channel" help="(-channel_131_description) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_tmt6plex_reference_channel" type="integer" min="126" max="131" optional="True" value="126" label="Number of the reference channel (126-131)" help="(-reference_channel) "/> - <repeat name="rep_param_tmt6plex_correction_matrix" min="0" max="1" title="param_tmt6plex_correction_matrix"> - <param name="param_tmt6plex_correction_matrix" type="text" size="30" 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="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> </param> - </repeat> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> - <param name="param_extraction_precursor_isotope_deviation" type="float" min="0.0" optional="True" 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="(-precursor_isotope_deviation) "/> - <param name="param_extraction_purity_interpolation" display="radio" type="select" optional="False" value="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="(-purity_interpolation) If set to false, only the precursor scan will be used"> - <option value="true" selected="true">true</option> - <option value="false">false</option> + <param name="reference_channel" argument="-tmt16plex:reference_channel" type="select" optional="false" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help=""> + <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"/> + </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"/> + <expand macro="list_string_san"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + </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"/> + <expand macro="list_string_san"/> + </param> + </section> + <expand macro="adv_opts_macro"> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> </param> </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> + </param> </inputs> <outputs> - <data name="param_out" format="consensusxml"/> + <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> - <help>Calculates isobaric quantitative values for peptides + <tests> + <expand macro="autotest_IsobaricAnalyzer"/> + <expand macro="manutest_IsobaricAnalyzer"/> + </tests> + <help><![CDATA[Calculates isobaric quantitative values for peptides -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IsobaricAnalyzer.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_IsobaricAnalyzer.html]]></help> + <expand macro="references"/> </tool>