Mercurial > repos > galaxyp > openms_metabolitespectralmatcher

annotate MetaboliteSpectralMatcher.xml @ 13:75ccdbc2475d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:02:30 +0000
parents d8503d5dd2ba
children e46a9e72c395
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Perform a spectral library search.</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="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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16 ## Preprocessing
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 mkdir database &&
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20 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
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21 mkdir out &&
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23 ## Main program call
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 -database
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32 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
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33 -out
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34 'out/output.${gxy2omsext("mztab")}'
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35
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36 ## Postprocessing
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37 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
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38 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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39 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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40 #end if]]></command>
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41 <configfiles>
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42 <inputs name="args_json" data_style="paths"/>
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43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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44 </configfiles>
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45 <inputs>
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46 <param argument="-in" type="data" format="mzml" optional="false" label="Input spectra" help=" select mzml data sets(s)"/>
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47 <param argument="-database" type="data" format="mzml" optional="false" label="Default spectral database" help=" select mzml data sets(s)"/>
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48 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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49 <param name="prec_mass_error_value" argument="-algorithm:prec_mass_error_value" type="float" optional="true" value="100.0" label="Error allowed for precursor ion mass" help=""/>
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50 <param name="frag_mass_error_value" argument="-algorithm:frag_mass_error_value" type="float" optional="true" value="500.0" label="Error allowed for product ions" help=""/>
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51 <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="true" label="Unit of mass error (ppm or Da)" help="">
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52 <option value="ppm" selected="true">ppm</option>
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53 <option value="Da">Da</option>
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54 <expand macro="list_string_san" name="mass_error_unit"/>
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55 </param>
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56 <param name="report_mode" argument="-algorithm:report_mode" type="select" optional="true" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
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57 <option value="top3" selected="true">top3</option>
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58 <option value="best">best</option>
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59 <expand macro="list_string_san" name="report_mode"/>
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60 </param>
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61 <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="true" label="Positive or negative ionization mode?" help="">
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62 <option value="positive" selected="true">positive</option>
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63 <option value="negative">negative</option>
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64 <expand macro="list_string_san" name="ionization_mode"/>
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65 </param>
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66 </section>
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67 <expand macro="adv_opts_macro">
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68 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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69 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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70 <expand macro="list_string_san" name="test"/>
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71 </param>
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72 </expand>
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73 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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74 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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75 </param>
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76 </inputs>
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77 <outputs>
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78 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
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79 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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80 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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81 </data>
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82 </outputs>
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83 <tests><!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
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84 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
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85 <param name="adv_opts|test" value="true"/>
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86 <param name="in" ftype="mzml" value="spectra.mzML"/>
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87 <param name="database" value="MetaboliteSpectralDB.mzML"/>
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88 <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/>
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89 </test>
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90 </tests>
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91 <help><![CDATA[Perform a spectral library search.
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92
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93
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94 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaboliteSpectralMatcher.html]]></help>
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95 <expand macro="references"/>
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96 </tool>