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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
| author | bgruening |
|---|---|
| date | Wed, 27 Jan 2016 10:06:49 -0500 |
| parents | 3d84209d3178 |
| children |
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<?xml version="1.0" encoding="UTF-8"?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> <!--Proposed Tool Section: [Quantitation]--> <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.0.0"> <description>Calculates isobaric quantitative values for peptides</description> <macros> <token name="@EXECUTABLE@">IsobaricAnalyzer</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>IsobaricAnalyzer #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 -threads \${GALAXY_SLOTS:-24} #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 #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 #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 #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 #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 #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 $param_tmt6plex_channel_126_description: -tmt6plex:channel_126_description "$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 #end if #end if </command> <inputs> <param help="(-type) " label="Isobaric Quantitation method used in the experiment" name="param_type" optional="True" type="select" value="itraq4plex"> <option value="itraq4plex">itraq4plex</option> <option value="itraq8plex">itraq8plex</option> <option value="tmt10plex">tmt10plex</option> <option value="tmt6plex">tmt6plex</option> </param> <param format="mzml" help="(-in) " label="input raw/picked data file" name="param_in" optional="False" type="data"/> <param help="(-select_activation) e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering" label="Operate only on MSn scans where any of its precursors features a certain activation method (" name="param_extraction_select_activation" optional="True" type="select" value="High-energy collision-induced dissociation"> <option value="Collision-induced dissociation">Collision-induced dissociation</option> <option value="Post-source decay">Post-source decay</option> <option value="Plasma desorption">Plasma desorption</option> <option value="Surface-induced dissociation">Surface-induced dissociation</option> <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> <option value="Electron capture dissociation">Electron capture dissociation</option> <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> <option value="Photodissociation">Photodissociation</option> <option value="Electron transfer dissociation">Electron transfer dissociation</option> <option value=""></option> </param> <param help="(-reporter_mass_shift) " label="Allowed shift (left to right) in Da from the expected position" max="0.5" min="1e-08" name="param_extraction_reporter_mass_shift" optional="True" type="float" value="0.1"/> <param help="(-min_precursor_intensity) MS/MS scans having a precursor with a lower intensity will not be considered for quantitation" label="Minimum intensity of the precursor to be extracted" min="0.0" name="param_extraction_min_precursor_intensity" optional="True" type="float" value="1.0"/> <param checked="true" falsevalue="" help="(-keep_unannotated_precursor) " label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" name="param_extraction_keep_unannotated_precursor" optional="True" truevalue="-extraction:keep_unannotated_precursor" type="boolean"/> <param help="(-min_reporter_intensity) " label="Minimum intensity of the individual reporter ions to be extracted" min="0.0" name="param_extraction_min_reporter_intensity" optional="True" type="float" value="0.0"/> <param checked="false" falsevalue="" help="(-discard_low_intensity_quantifications) " label="Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'" name="param_extraction_discard_low_intensity_quantifications" optional="True" truevalue="-extraction:discard_low_intensity_quantifications" type="boolean"/> <param help="(-min_precursor_purity) " label="Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precurso" max="1.0" min="0.0" name="param_extraction_min_precursor_purity" optional="True" type="float" value="0.0"/> <param help="(-channel_114_description) " label="Description for the content of the 114 channel" name="param_itraq4plex_channel_114_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_115_description) " label="Description for the content of the 115 channel" name="param_itraq4plex_channel_115_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_116_description) " label="Description for the content of the 116 channel" name="param_itraq4plex_channel_116_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_117_description) " label="Description for the content of the 117 channel" name="param_itraq4plex_channel_117_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-reference_channel) " label="Number of the reference channel (114-117)" max="117" min="114" name="param_itraq4plex_reference_channel" optional="True" type="integer" value="114"/> <repeat max="1" min="0" name="rep_param_itraq4plex_correction_matrix" title="param_itraq4plex_correction_matrix"> <param help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" name="param_itraq4plex_correction_matrix" size="30" 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"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <param help="(-channel_113_description) " label="Description for the content of the 113 channel" name="param_itraq8plex_channel_113_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_114_description) " label="Description for the content of the 114 channel" name="param_itraq8plex_channel_114_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_115_description) " label="Description for the content of the 115 channel" name="param_itraq8plex_channel_115_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_116_description) " label="Description for the content of the 116 channel" name="param_itraq8plex_channel_116_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_117_description) " label="Description for the content of the 117 channel" name="param_itraq8plex_channel_117_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_118_description) " label="Description for the content of the 118 channel" name="param_itraq8plex_channel_118_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_119_description) " label="Description for the content of the 119 channel" name="param_itraq8plex_channel_119_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_121_description) " label="Description for the content of the 121 channel" name="param_itraq8plex_channel_121_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-reference_channel) Please note that 120 is not valid" label="Number of the reference channel (113-121)" max="121" min="113" name="param_itraq8plex_reference_channel" optional="True" type="integer" value="113"/> <repeat max="1" min="0" name="rep_param_itraq8plex_correction_matrix" title="param_itraq8plex_correction_matrix"> <param help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" name="param_itraq8plex_correction_matrix" size="30" 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"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <param checked="true" falsevalue="" help="(-isotope_correction) Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results" label="Enable isotope correction (highly recommended)" name="param_quantification_isotope_correction" optional="True" truevalue="-quantification:isotope_correction" type="boolean"/> <param checked="false" falsevalue="" 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!" label="Enable normalization of channel intensities with respect to the reference channel" name="param_quantification_normalization" optional="True" truevalue="-quantification:normalization" type="boolean"/> <param help="(-channel_126_description) " label="Description for the content of the 126 channel" name="param_tmt10plex_channel_126_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_127N_description) " label="Description for the content of the 127N channel" name="param_tmt10plex_channel_127N_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_127C_description) " label="Description for the content of the 127C channel" name="param_tmt10plex_channel_127C_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_128N_description) " label="Description for the content of the 128N channel" name="param_tmt10plex_channel_128N_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_128C_description) " label="Description for the content of the 128C channel" name="param_tmt10plex_channel_128C_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_129N_description) " label="Description for the content of the 129N channel" name="param_tmt10plex_channel_129N_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_129C_description) " label="Description for the content of the 129C channel" name="param_tmt10plex_channel_129C_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_130N_description) " label="Description for the content of the 130N channel" name="param_tmt10plex_channel_130N_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_130C_description) " label="Description for the content of the 130C channel" name="param_tmt10plex_channel_130C_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_131_description) " label="Description for the content of the 131 channel" name="param_tmt10plex_channel_131_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-reference_channel) " label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" name="param_tmt10plex_reference_channel" optional="True" type="select" value="126"> <option value="126">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 max="1" min="0" name="rep_param_tmt10plex_correction_matrix" title="param_tmt10plex_correction_matrix"> <param help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" name="param_tmt10plex_correction_matrix" size="30" 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"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <param help="(-channel_126_description) " label="Description for the content of the 126 channel" name="param_tmt6plex_channel_126_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_127_description) " label="Description for the content of the 127 channel" name="param_tmt6plex_channel_127_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_128_description) " label="Description for the content of the 128 channel" name="param_tmt6plex_channel_128_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_129_description) " label="Description for the content of the 129 channel" name="param_tmt6plex_channel_129_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_130_description) " label="Description for the content of the 130 channel" name="param_tmt6plex_channel_130_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-channel_131_description) " label="Description for the content of the 131 channel" name="param_tmt6plex_channel_131_description" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-reference_channel) " label="Number of the reference channel (126-131)" max="131" min="126" name="param_tmt6plex_reference_channel" optional="True" type="integer" value="126"/> <repeat max="1" min="0" name="rep_param_tmt6plex_correction_matrix" title="param_tmt6plex_correction_matrix"> <param help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" name="param_tmt6plex_correction_matrix" size="30" 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"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <expand macro="advanced_options"> <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> <param help="(-precursor_isotope_deviation) " 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" min="0.0" name="param_extraction_precursor_isotope_deviation" optional="True" type="float" value="10.0"/> <param checked="true" falsevalue="" help="(-purity_interpolation) If set to false, only the precursor scan will be used" 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" name="param_extraction_purity_interpolation" optional="True" truevalue="-extraction:purity_interpolation" type="boolean"/> </expand> </inputs> <outputs> <data format="consensusxml" name="param_out"/> </outputs> <help>Calculates isobaric quantitative values for peptides For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IsobaricAnalyzer.html</help> </tool>