Mercurial > repos > galaxyp > openms_qcextractor
comparison QCExtractor.xml @ 12:c8d22d876c75 draft
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 19:00:36 +0000 |
parents | 7468a1c8ca6e |
children | 9a527fdadffc |
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11:a1d6562ac8cf | 12:c8d22d876c75 |
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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="QCExtractor" name="QCExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="QCExtractor" name="QCExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Extracts a table attachment to a given qc parameter.</description> | 5 <description>Extracts a table attachment to a given qc parameter.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">QCExtractor</token> | 7 <token name="@EXECUTABLE@">QCExtractor</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@ |
47 <configfiles> | 45 <configfiles> |
48 <inputs name="args_json" data_style="paths"/> | 46 <inputs name="args_json" data_style="paths"/> |
49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
50 </configfiles> | 48 </configfiles> |
51 <inputs> | 49 <inputs> |
52 <param name="in" argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/> | 50 <param argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/> |
53 <param name="qp" argument="-qp" type="text" optional="false" value="" label="Target attachment qp" help=""> | 51 <param argument="-qp" type="text" optional="false" value="" label="Target attachment qp" help=""> |
54 <expand macro="list_string_san"/> | 52 <expand macro="list_string_san" name="qp"/> |
55 </param> | 53 </param> |
56 <param name="run" argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/> | 54 <param argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/> |
57 <param name="name" argument="-name" type="text" optional="true" value="" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help=""> | 55 <param argument="-name" type="text" optional="true" value="" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help=""> |
58 <expand macro="list_string_san"/> | 56 <expand macro="list_string_san" name="name"/> |
59 </param> | 57 </param> |
60 <expand macro="adv_opts_macro"> | 58 <expand macro="adv_opts_macro"> |
61 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 59 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
62 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 60 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
63 <expand macro="list_string_san"/> | 61 <expand macro="list_string_san" name="test"/> |
64 </param> | 62 </param> |
65 </expand> | 63 </expand> |
66 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 64 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
67 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 65 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
68 </param> | 66 </param> |
71 <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"/> | 69 <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"/> |
72 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 70 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
73 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 71 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
74 </data> | 72 </data> |
75 </outputs> | 73 </outputs> |
76 <tests> | 74 <tests><!--TODO--> |
77 <expand macro="autotest_QCExtractor"/> | 75 </tests> |
78 <expand macro="manutest_QCExtractor"/> | |
79 </tests> | |
80 <help><![CDATA[Extracts a table attachment to a given qc parameter. | 76 <help><![CDATA[Extracts a table attachment to a given qc parameter. |
81 | 77 |
82 | 78 |
83 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_QCExtractor.html]]></help> | 79 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCExtractor.html]]></help> |
84 <expand macro="references"/> | 80 <expand macro="references"/> |
85 </tool> | 81 </tool> |