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view FeatureFinderMultiplex.xml @ 4:6ead64a594bd draft default tip
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="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.0.0"> <description>Determination of peak ratios in LC-MS data</description> <macros> <token name="@EXECUTABLE@">FeatureFinderMultiplex</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>FeatureFinderMultiplex #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if #if $param_out_features: -out_features $param_out_features #end if #if $param_out_mzq: -out_mzq $param_out_mzq #end if -threads \${GALAXY_SLOTS:-24} #if $param_algorithm_labels: -algorithm:labels "$param_algorithm_labels" #end if #if $param_algorithm_charge: -algorithm:charge "$param_algorithm_charge" #end if #if $param_algorithm_rt_typical: -algorithm:rt_typical $param_algorithm_rt_typical #end if #if $param_algorithm_rt_min: -algorithm:rt_min $param_algorithm_rt_min #end if #if $param_algorithm_mz_tolerance: -algorithm:mz_tolerance $param_algorithm_mz_tolerance #end if #if $param_algorithm_mz_unit: -algorithm:mz_unit #if " " in str($param_algorithm_mz_unit): "$param_algorithm_mz_unit" #else $param_algorithm_mz_unit #end if #end if #if $param_algorithm_intensity_cutoff: -algorithm:intensity_cutoff $param_algorithm_intensity_cutoff #end if #if $param_algorithm_peptide_similarity: -algorithm:peptide_similarity $param_algorithm_peptide_similarity #end if #if $param_algorithm_averagine_similarity: -algorithm:averagine_similarity $param_algorithm_averagine_similarity #end if #if $param_algorithm_missed_cleavages: -algorithm:missed_cleavages $param_algorithm_missed_cleavages #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #if $adv_opts.param_algorithm_isotopes_per_peptide: -algorithm:isotopes_per_peptide "$adv_opts.param_algorithm_isotopes_per_peptide" #end if #if $adv_opts.param_algorithm_averagine_similarity_scaling: -algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling #end if #if $adv_opts.param_algorithm_knock_out: -algorithm:knock_out #end if #if $adv_opts.param_labels_Arg6: -labels:Arg6 $adv_opts.param_labels_Arg6 #end if #if $adv_opts.param_labels_Arg10: -labels:Arg10 $adv_opts.param_labels_Arg10 #end if #if $adv_opts.param_labels_Lys4: -labels:Lys4 $adv_opts.param_labels_Lys4 #end if #if $adv_opts.param_labels_Lys6: -labels:Lys6 $adv_opts.param_labels_Lys6 #end if #if $adv_opts.param_labels_Lys8: -labels:Lys8 $adv_opts.param_labels_Lys8 #end if #if $adv_opts.param_labels_Dimethyl0: -labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0 #end if #if $adv_opts.param_labels_Dimethyl4: -labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4 #end if #if $adv_opts.param_labels_Dimethyl6: -labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6 #end if #if $adv_opts.param_labels_Dimethyl8: -labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8 #end if #if $adv_opts.param_labels_ICPL0: -labels:ICPL0 $adv_opts.param_labels_ICPL0 #end if #if $adv_opts.param_labels_ICPL4: -labels:ICPL4 $adv_opts.param_labels_ICPL4 #end if #if $adv_opts.param_labels_ICPL6: -labels:ICPL6 $adv_opts.param_labels_ICPL6 #end if #if $adv_opts.param_labels_ICPL10: -labels:ICPL10 $adv_opts.param_labels_ICPL10 #end if #end if </command> <inputs> <param format="mzml" help="(-in) " label="LC-MS dataset in centroid or profile mode" name="param_in" optional="False" type="data"/> <param help="(-labels) [...] specifies the labels for a single sample. For example <br> <br>[][Lys8,Arg10] ... SILAC <br>[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC <br>[Dimethyl0][Dimethyl6] ... Dimethyl <br>[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl <br>[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL" label="Labels used for labelling the samples" name="param_algorithm_labels" size="30" type="text" value="[][Lys8,Arg10]"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-charge) min charge : max charge" label="Range of charge states in the sample, i.e" name="param_algorithm_charge" size="30" type="text" value="1:4"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-rt_typical) (This is not an upper bound. Peptides that elute for longer will be reported.)" label="Typical retention time [s] over which a characteristic peptide elutes" min="0.0" name="param_algorithm_rt_typical" optional="True" type="float" value="40.0"/> <param help="(-rt_min) (Any peptides seen for a shorter time period are not reported.)" label="Lower bound for the retention time [s]" min="0.0" name="param_algorithm_rt_min" optional="True" type="float" value="2.0"/> <param help="(-mz_tolerance) " label="m/z tolerance for search of peak patterns" min="0.0" name="param_algorithm_mz_tolerance" optional="True" type="float" value="6.0"/> <param help="(-mz_unit) " label="Unit of the 'mz_tolerance' paramete" name="param_algorithm_mz_unit" optional="True" type="select" value="ppm"> <option value="Da">Da</option> <option value="ppm">ppm</option> </param> <param help="(-intensity_cutoff) " label="Lower bound for the intensity of isotopic peaks" min="0.0" name="param_algorithm_intensity_cutoff" optional="True" type="float" value="1000.0"/> <param help="(-peptide_similarity) This parameter is a lower bound on their similarity" label="Two peptides in a multiplet are expected to have the same isotopic pattern" max="1.0" min="-1.0" name="param_algorithm_peptide_similarity" optional="True" type="float" value="0.5"/> <param help="(-averagine_similarity) This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" max="1.0" min="-1.0" name="param_algorithm_averagine_similarity" optional="True" type="float" value="0.4"/> <param help="(-missed_cleavages) " label="Maximum number of missed cleavages due to incomplete digestion" min="0" name="param_algorithm_missed_cleavages" optional="True" type="integer" value="0"/> <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="(-isotopes_per_peptide) For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. " label="Range of isotopes per peptide in the sample" name="param_algorithm_isotopes_per_peptide" size="30" type="text" value="3:6"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-averagine_similarity_scaling) For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -> p' = p and x = 1 -> p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)" label="Let x denote this scaling factor, and p the averagine similarity paramete" max="1.0" min="0.0" name="param_algorithm_averagine_similarity_scaling" optional="True" type="float" value="0.75"/> <param checked="false" falsevalue="" help="(-knock_out) (Supported for doublex, triplex and quadruplex experiments only.)" label="Is it likely that knock-outs are present?" name="param_algorithm_knock_out" optional="True" truevalue="-algorithm:knock_out" type="boolean"/> <param help="(-Arg6) " label="Label:13C(6) | C(-6) 13C(6) | unimod #188" min="0.0" name="param_labels_Arg6" optional="True" type="float" value="6.0201290268"/> <param help="(-Arg10) " label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" min="0.0" name="param_labels_Arg10" optional="True" type="float" value="10.0082686"/> <param help="(-Lys4) " label="Label:2H(4) | H(-4) 2H(4) | unimod #481" min="0.0" name="param_labels_Lys4" optional="True" type="float" value="4.0251069836"/> <param help="(-Lys6) " label="Label:13C(6) | C(-6) 13C(6) | unimod #188" min="0.0" name="param_labels_Lys6" optional="True" type="float" value="6.0201290268"/> <param help="(-Lys8) " label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" min="0.0" name="param_labels_Lys8" optional="True" type="float" value="8.0141988132"/> <param help="(-Dimethyl0) " label="Dimethyl | H(4) C(2) | unimod #36" min="0.0" name="param_labels_Dimethyl0" optional="True" type="float" value="28.0313"/> <param help="(-Dimethyl4) " label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" min="0.0" name="param_labels_Dimethyl4" optional="True" type="float" value="32.056407"/> <param help="(-Dimethyl6) " label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" min="0.0" name="param_labels_Dimethyl6" optional="True" type="float" value="34.063117"/> <param help="(-Dimethyl8) " label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" min="0.0" name="param_labels_Dimethyl8" optional="True" type="float" value="36.07567"/> <param help="(-ICPL0) " label="ICPL | H(3) C(6) N O | unimod #365" min="0.0" name="param_labels_ICPL0" optional="True" type="float" value="105.021464"/> <param help="(-ICPL4) " label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" min="0.0" name="param_labels_ICPL4" optional="True" type="float" value="109.046571"/> <param help="(-ICPL6) " label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" min="0.0" name="param_labels_ICPL6" optional="True" type="float" value="111.041593"/> <param help="(-ICPL10) " label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" min="0.0" name="param_labels_ICPL10" optional="True" type="float" value="115.0667"/> </expand> </inputs> <outputs> <data format="consensusxml" name="param_out"/> <data format="xml" name="param_out_features"/> <data format="mzq" name="param_out_mzq"/> </outputs> <help>Determination of peak ratios in LC-MS data For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMultiplex.html</help> </tool>