Mercurial > repos > galaxyp > openms_metabolitespectralmatcher

annotate MetaboliteSpectralMatcher.xml @ 0:d2b1258ee673 draft

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author galaxyp
date Wed, 01 Mar 2017 12:16:51 -0500
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d2b1258ee673 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="2.1.0">
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5 <description>Find potential HMDB ids within the given mass error window.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>MetaboliteSpectralMatcher
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_algorithm_prec_mass_error_value:
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22 -algorithm:prec_mass_error_value $param_algorithm_prec_mass_error_value
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23 #end if
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24 #if $param_algorithm_frag_mass_error_value:
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25 -algorithm:frag_mass_error_value $param_algorithm_frag_mass_error_value
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26 #end if
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27 #if $param_algorithm_mass_error_unit:
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28 -algorithm:mass_error_unit $param_algorithm_mass_error_unit
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29 #end if
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30 #if $param_algorithm_report_mode:
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31 -algorithm:report_mode $param_algorithm_report_mode
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32 #end if
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33 #if $param_algorithm_ionization_mode:
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34 -algorithm:ionization_mode $param_algorithm_ionization_mode
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35 #end if
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36 #if $adv_opts.adv_opts_selector=='advanced':
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37 #if $adv_opts.param_force:
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38 -force
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39 #end if
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40 #end if
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41 </command>
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42 <inputs>
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43 <param name="param_in" type="data" format="mzml" optional="False" label="mzML file" help="(-in) "/>
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44 <param name="param_algorithm_prec_mass_error_value" type="float" value="100.0" label="Error allowed for precursor ion mass" help="(-prec_mass_error_value) "/>
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45 <param name="param_algorithm_frag_mass_error_value" type="float" value="500.0" label="Error allowed for product ions" help="(-frag_mass_error_value) "/>
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46 <param name="param_algorithm_mass_error_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) ">
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47 <option value="ppm" selected="true">ppm</option>
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48 <option value="Da">Da</option>
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49 </param>
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50 <param name="param_algorithm_report_mode" display="radio" type="select" optional="False" value="top3" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="(-report_mode) ">
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51 <option value="top3" selected="true">top3</option>
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52 <option value="best">best</option>
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53 </param>
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54 <param name="param_algorithm_ionization_mode" display="radio" type="select" optional="False" value="positive" label="Positive or negative ionization mode?" help="(-ionization_mode) ">
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55 <option value="positive" selected="true">positive</option>
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56 <option value="negative">negative</option>
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57 </param>
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58 <expand macro="advanced_options">
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59 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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60 </expand>
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61 </inputs>
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62 <outputs>
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63 <data name="param_out" format="tabular"/>
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64 </outputs>
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65 <help>Find potential HMDB ids within the given mass error window.
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66
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67
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68 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaboliteSpectralMatcher.html</help>
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69 </tool>