Mercurial > repos > galaxyp > openms_spectrastsearchadapter

annotate SpectraSTSearchAdapter.xml @ 0:369f340978e4 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:11:13 -0400
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369f340978e4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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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="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="2.2.0.1">
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5 <description>Interface to the SEARCH Mode of the SpectraST executable</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SpectraSTSearchAdapter</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>SpectraSTSearchAdapter
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14
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15 -spectra_files
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16 #for token in $param_spectra_files:
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17 $token
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18 #end for
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19
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20 #if $rep_param_output_files:
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21 -output_files
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22 #for token in $rep_param_output_files:
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23 #if " " in str(token):
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24 "$token.param_output_files"
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25 #else
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26 $token.param_output_files
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27 #end if
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28 #end for
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29 #end if
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30 #if $param_library_file:
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31 -library_file $param_library_file
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32 #end if
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33 #if $param_sequence_database_file:
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34 -sequence_database_file $param_sequence_database_file
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35 #end if
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36 #if $param_sequence_database_type:
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37 -sequence_database_type
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38 #if " " in str($param_sequence_database_type):
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39 "$param_sequence_database_type"
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40 #else
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41 $param_sequence_database_type
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42 #end if
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43 #end if
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44 #if $param_search_file:
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45 -search_file $param_search_file
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46 #end if
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47 #if $param_params_file:
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48 -params_file $param_params_file
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49 #end if
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50 #if $param_precursor_mz_tolerance:
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51 -precursor_mz_tolerance $param_precursor_mz_tolerance
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52 #end if
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53 #if $adv_opts.adv_opts_selector=='advanced':
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54 #if $adv_opts.param_use_isotopically_averaged_mass:
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55 -use_isotopically_averaged_mass
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56 #end if
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57 #if $adv_opts.param_use_all_charge_states:
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58 -use_all_charge_states
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59 #end if
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60 #if $adv_opts.param_user_mod_file:
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61 -user_mod_file $adv_opts.param_user_mod_file
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62 #end if
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63 #if $adv_opts.param_force:
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64 -force
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65 #end if
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66 #end if
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67 </command>
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68 <inputs>
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69 <param name="param_spectra_files" type="data" format="mzml,mzxml,mzData,dta,msp" multiple="true" optional="False" size="30" label="File names(s) of spectra to be searched" help="(-spectra_files) ">
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70 <sanitizer>
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71 <valid initial="string.printable">
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72 <remove value="'"/>
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73 <remove value="&quot;"/>
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74 </valid>
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75 </sanitizer>
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76 </param>
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77 <param name="param_library_file" type="data" format="splib" optional="False" label="Specify library file" help="(-library_file) "/>
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78 <param name="param_sequence_database_file" type="data" format="fasta" optional="True" label="The sequence database" help="(-sequence_database_file) "/>
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79 <param name="param_sequence_database_type" display="radio" type="select" optional="False" value="AA" label="Specify type of sequence database" help="(-sequence_database_type) ">
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80 <option value="DNA">DNA</option>
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81 <option value="AA" selected="true">AA</option>
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82 </param>
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83 <param name="param_search_file" type="data" format="txt,dat" optional="True" label="Only search a subset of the query spectra in the search file" help="(-search_file) "/>
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84 <param name="param_params_file" type="data" format="params" optional="True" label="Read search options from file" help="(-params_file) All options set in the file will be overridden by command-line options, if specified"/>
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85 <param name="param_precursor_mz_tolerance" type="float" min="0.0" optional="True" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="(-precursor_mz_tolerance) Monoisotopic mass is assumed"/>
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86 <expand macro="advanced_options">
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87 <param name="param_use_isotopically_averaged_mass" display="radio" type="boolean" truevalue="-use_isotopically_averaged_mass" falsevalue="" checked="false" optional="True" label="Use isotopically averaged mass instead of monoisotopic mass" help="(-use_isotopically_averaged_mass) "/>
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88 <param name="param_use_all_charge_states" display="radio" type="boolean" truevalue="-use_all_charge_states" falsevalue="" checked="false" optional="True" label="Search library spectra of all charge states, i.e., ignore specified charge state (if any) of the query spectrum" help="(-use_all_charge_states) "/>
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89 <param name="param_user_mod_file" type="data" format="txt" label="Specify name of user-defined modifications file" help="(-user_mod_file) Default is &quot;spectrast.usermods&quot;"/>
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90 <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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91 </expand>
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92 </inputs>
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93 <outputs>
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94 <data name="param_output_files" format="txt"/>
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95 </outputs>
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96 <help>Interface to the SEARCH Mode of the SpectraST executable
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97
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98
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99 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpectraSTSearchAdapter.html</help>
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100 </tool>