Mercurial > repos > galaxyp > openms_metabolitespectralmatcher

comparison MetaboliteSpectralMatcher.xml @ 9:7b5df538705e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:24:57 +0000
parents 867d97b37983
children d8503d5dd2ba
comparison
equal deleted inserted replaced
8:da8c663a5564 9:7b5df538705e
1 <?xml version='1.0' encoding='UTF-8'?> 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 CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="2.3.0"> 4 <tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Perform a spectral library search.</description> 5 <description>Perform a spectral library search.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token> 7 <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[MetaboliteSpectralMatcher 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_database: 21 mkdir database &&
19 -database $param_database 22 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
20 #end if 23 mkdir out &&
21 #if $param_out: 24
22 -out $param_out 25 ## Main program call
23 #end if 26
24 #if $param_algorithm_prec_mass_error_value: 27 set -o pipefail &&
25 -algorithm:prec_mass_error_value $param_algorithm_prec_mass_error_value 28 @EXECUTABLE@ -write_ctd ./ &&
26 #end if 29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
27 #if $param_algorithm_frag_mass_error_value: 30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
28 -algorithm:frag_mass_error_value $param_algorithm_frag_mass_error_value 31 -in
29 #end if 32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
30 #if $param_algorithm_mass_error_unit: 33 -database
31 -algorithm:mass_error_unit 34 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
32 #if " " in str($param_algorithm_mass_error_unit): 35 -out
33 "$param_algorithm_mass_error_unit" 36 'out/output.${gxy2omsext("mztab")}'
34 #else 37
35 $param_algorithm_mass_error_unit 38 ## Postprocessing
36 #end if 39 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
37 #end if 40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
38 #if $param_algorithm_report_mode: 41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
39 -algorithm:report_mode 42 #end if]]></command>
40 #if " " in str($param_algorithm_report_mode): 43 <configfiles>
41 "$param_algorithm_report_mode" 44 <inputs name="args_json" data_style="paths"/>
42 #else 45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
43 $param_algorithm_report_mode 46 </configfiles>
44 #end if
45 #end if
46 #if $param_algorithm_ionization_mode:
47 -algorithm:ionization_mode
48 #if " " in str($param_algorithm_ionization_mode):
49 "$param_algorithm_ionization_mode"
50 #else
51 $param_algorithm_ionization_mode
52 #end if
53 #end if
54 #if $adv_opts.adv_opts_selector=='advanced':
55 #if $adv_opts.param_force:
56 -force
57 #end if
58 #end if
59 ]]></command>
60 <inputs> 47 <inputs>
61 <param name="param_in" type="data" format="mzml" optional="False" label="Input spectra" help="(-in) "/> 48 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input spectra" help=" select mzml data sets(s)"/>
62 <param name="param_database" type="data" format="mzml" optional="True" value="CHEMISTRY/MetaboliteSpectralDB.mzML" label="Default spectral database" help="(-database) "/> 49 <param name="database" argument="-database" type="data" format="mzml" optional="false" label="Default spectral database" help=" select mzml data sets(s)"/>
63 <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) "/> 50 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
64 <param name="param_algorithm_frag_mass_error_value" type="float" value="500.0" label="Error allowed for product ions" help="(-frag_mass_error_value) "/> 51 <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=""/>
65 <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) "> 52 <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=""/>
66 <option value="ppm" selected="true">ppm</option> 53 <param name="mass_error_unit" argument="-algorithm:mass_error_unit" display="radio" type="select" optional="false" label="Unit of mass error (ppm or Da)" help="">
67 <option value="Da">Da</option> 54 <option value="ppm" selected="true">ppm</option>
55 <option value="Da">Da</option>
56 <expand macro="list_string_san"/>
57 </param>
58 <param name="report_mode" argument="-algorithm:report_mode" display="radio" type="select" optional="false" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
59 <option value="top3" selected="true">top3</option>
60 <option value="best">best</option>
61 <expand macro="list_string_san"/>
62 </param>
63 <param name="ionization_mode" argument="-algorithm:ionization_mode" display="radio" type="select" optional="false" label="Positive or negative ionization mode?" help="">
64 <option value="positive" selected="true">positive</option>
65 <option value="negative">negative</option>
66 <expand macro="list_string_san"/>
67 </param>
68 </section>
69 <expand macro="adv_opts_macro">
70 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
71 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
72 <expand macro="list_string_san"/>
73 </param>
74 </expand>
75 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
76 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
68 </param> 77 </param>
69 <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) ">
70 <option value="top3" selected="true">top3</option>
71 <option value="best">best</option>
72 </param>
73 <param name="param_algorithm_ionization_mode" display="radio" type="select" optional="False" value="positive" label="Positive or negative ionization mode?" help="(-ionization_mode) ">
74 <option value="positive" selected="true">positive</option>
75 <option value="negative">negative</option>
76 </param>
77 <expand macro="advanced_options">
78 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
79 </expand>
80 </inputs> 78 </inputs>
81 <outputs> 79 <outputs>
82 <data name="param_out" format="tabular"/> 80 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
81 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
82 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
83 </data>
83 </outputs> 84 </outputs>
84 <help>Perform a spectral library search. 85 <tests>
86 <expand macro="autotest_MetaboliteSpectralMatcher"/>
87 <expand macro="manutest_MetaboliteSpectralMatcher"/>
88 </tests>
89 <help><![CDATA[Perform a spectral library search.
85 90
86 91
87 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MetaboliteSpectralMatcher.html</help> 92 For more information, visit http://www.openms.de/documentation/UTILS_MetaboliteSpectralMatcher.html]]></help>
93 <expand macro="references"/>
88 </tool> 94 </tool>