Mercurial > repos > galaxyp > openms_spectrastsearchadapter
comparison SpectraSTSearchAdapter.xml @ 0:369f340978e4 draft
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 |
| parents | |
| children | c54dbaf4802b |
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| -1:000000000000 | 0:369f340978e4 |
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| 1 <?xml version='1.0' encoding='UTF-8'?> | |
| 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> | |
| 3 <!--Proposed Tool Section: [Utilities]--> | |
| 4 <tool id="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="2.2.0.1"> | |
| 5 <description>Interface to the SEARCH Mode of the SpectraST executable</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">SpectraSTSearchAdapter</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>SpectraSTSearchAdapter | |
| 14 | |
| 15 -spectra_files | |
| 16 #for token in $param_spectra_files: | |
| 17 $token | |
| 18 #end for | |
| 19 | |
| 20 #if $rep_param_output_files: | |
| 21 -output_files | |
| 22 #for token in $rep_param_output_files: | |
| 23 #if " " in str(token): | |
| 24 "$token.param_output_files" | |
| 25 #else | |
| 26 $token.param_output_files | |
| 27 #end if | |
| 28 #end for | |
| 29 #end if | |
| 30 #if $param_library_file: | |
| 31 -library_file $param_library_file | |
| 32 #end if | |
| 33 #if $param_sequence_database_file: | |
| 34 -sequence_database_file $param_sequence_database_file | |
| 35 #end if | |
| 36 #if $param_sequence_database_type: | |
| 37 -sequence_database_type | |
| 38 #if " " in str($param_sequence_database_type): | |
| 39 "$param_sequence_database_type" | |
| 40 #else | |
| 41 $param_sequence_database_type | |
| 42 #end if | |
| 43 #end if | |
| 44 #if $param_search_file: | |
| 45 -search_file $param_search_file | |
| 46 #end if | |
| 47 #if $param_params_file: | |
| 48 -params_file $param_params_file | |
| 49 #end if | |
| 50 #if $param_precursor_mz_tolerance: | |
| 51 -precursor_mz_tolerance $param_precursor_mz_tolerance | |
| 52 #end if | |
| 53 #if $adv_opts.adv_opts_selector=='advanced': | |
| 54 #if $adv_opts.param_use_isotopically_averaged_mass: | |
| 55 -use_isotopically_averaged_mass | |
| 56 #end if | |
| 57 #if $adv_opts.param_use_all_charge_states: | |
| 58 -use_all_charge_states | |
| 59 #end if | |
| 60 #if $adv_opts.param_user_mod_file: | |
| 61 -user_mod_file $adv_opts.param_user_mod_file | |
| 62 #end if | |
| 63 #if $adv_opts.param_force: | |
| 64 -force | |
| 65 #end if | |
| 66 #end if | |
| 67 </command> | |
| 68 <inputs> | |
| 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) "> | |
| 70 <sanitizer> | |
| 71 <valid initial="string.printable"> | |
| 72 <remove value="'"/> | |
| 73 <remove value="""/> | |
| 74 </valid> | |
| 75 </sanitizer> | |
| 76 </param> | |
| 77 <param name="param_library_file" type="data" format="splib" optional="False" label="Specify library file" help="(-library_file) "/> | |
| 78 <param name="param_sequence_database_file" type="data" format="fasta" optional="True" label="The sequence database" help="(-sequence_database_file) "/> | |
| 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) "> | |
| 80 <option value="DNA">DNA</option> | |
| 81 <option value="AA" selected="true">AA</option> | |
| 82 </param> | |
| 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) "/> | |
| 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"/> | |
| 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"/> | |
| 86 <expand macro="advanced_options"> | |
| 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) "/> | |
| 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) "/> | |
| 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 "spectrast.usermods""/> | |
| 90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
| 91 </expand> | |
| 92 </inputs> | |
| 93 <outputs> | |
| 94 <data name="param_output_files" format="txt"/> | |
| 95 </outputs> | |
| 96 <help>Interface to the SEARCH Mode of the SpectraST executable | |
| 97 | |
| 98 | |
| 99 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpectraSTSearchAdapter.html</help> | |
| 100 </tool> |