Mercurial > repos > galaxyp > openms_speclibcreator
comparison SpecLibCreator.xml @ 13:da1fa8ce2d96 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:07:29 +0000 |
parents | 5d837ca93d0e |
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12:7895c4fbe46d | 13:da1fa8ce2d96 |
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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="SpecLibCreator" name="SpecLibCreator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="SpecLibCreator" name="SpecLibCreator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Creates an MSP formatted spectral library.</description> | 5 <description>Creates an MSP formatted spectral library.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">SpecLibCreator</token> | 7 <token name="@EXECUTABLE@">SpecLibCreator</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
11 </macros> | 9 </macros> |
12 <expand macro="requirements"/> | 10 <expand macro="requirements"/> |
13 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
15 @EXT_FOO@ | 13 @EXT_FOO@ |
43 <configfiles> | 41 <configfiles> |
44 <inputs name="args_json" data_style="paths"/> | 42 <inputs name="args_json" data_style="paths"/> |
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
46 </configfiles> | 44 </configfiles> |
47 <inputs> | 45 <inputs> |
48 <param name="info" argument="-info" type="data" format="csv" optional="false" label="Holds id, peptide, retention time etc" help=" select csv data sets(s)"/> | 46 <param argument="-info" type="data" format="csv" optional="false" label="Holds id, peptide, retention time etc" help=" select csv data sets(s)"/> |
49 <param name="itemseperator" argument="-itemseperator" type="text" optional="true" value="," label=" Separator between items. e.g. ," help=""> | 47 <param argument="-itemseperator" type="text" optional="true" value="," label=" Separator between items. e.g. ," help=""> |
50 <expand macro="list_string_san"/> | 48 <expand macro="list_string_san" name="itemseperator"/> |
51 </param> | 49 </param> |
52 <param name="itemenclosed" argument="-itemenclosed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="'true' or 'false' if true every item is enclosed" help="e.g. '$peptide$,$run$"/> | 50 <param argument="-itemenclosed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="'true' or 'false' if true every item is enclosed" help="e.g. '$peptide$,$run$"/> |
53 <param name="spec" argument="-spec" type="data" format="mzdata,mzxml" optional="false" label="spectra" help=" select mzdata,mzxml data sets(s)"/> | 51 <param argument="-spec" type="data" format="mzdata,mzxml" optional="false" label="spectra" help=" select mzdata,mzxml data sets(s)"/> |
54 <expand macro="adv_opts_macro"> | 52 <expand macro="adv_opts_macro"> |
55 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
56 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 54 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
57 <expand macro="list_string_san"/> | 55 <expand macro="list_string_san" name="test"/> |
58 </param> | 56 </param> |
59 </expand> | 57 </expand> |
60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
62 </param> | 60 </param> |
65 <data name="out" label="${tool.name} on ${on_string}: out" format="msp"/> | 63 <data name="out" label="${tool.name} on ${on_string}: out" format="msp"/> |
66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
68 </data> | 66 </data> |
69 </outputs> | 67 </outputs> |
70 <tests> | 68 <tests><!--TODO could not find test data --> |
71 <expand macro="autotest_SpecLibCreator"/> | 69 </tests> |
72 <expand macro="manutest_SpecLibCreator"/> | |
73 </tests> | |
74 <help><![CDATA[Creates an MSP formatted spectral library. | 70 <help><![CDATA[Creates an MSP formatted spectral library. |
75 | 71 |
76 | 72 |
77 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SpecLibCreator.html]]></help> | 73 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SpecLibCreator.html]]></help> |
78 <expand macro="references"/> | 74 <expand macro="references"/> |
79 </tool> | 75 </tool> |