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comparison QCExporter.xml @ 13:838b8e375587 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:15:54 +0000
parents adf7f5301284
children bb22e965eb5a
comparison
equal deleted inserted replaced
12:47e8f2bfa37f 13:838b8e375587
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="QCExporter" name="QCExporter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="QCExporter" name="QCExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Will extract several qp from several run/sets in a tabular format.</description> 5 <description>Will extract several qp from several run/sets in a tabular format.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">QCExporter</token> 7 <token name="@EXECUTABLE@">QCExporter</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="in" argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/> 46 <param argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/>
49 <param name="names" argument="-names" type="text" optional="true" value="" label="The name of the target runs or sets to be exported from" help="If empty, from all will be exported (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 47 <param argument="-names" type="text" optional="true" value="" label="The name of the target runs or sets to be exported from" help="If empty, from all will be exported (space separated list, in order to allow for spaces in list items surround them by single quotes)">
50 <expand macro="list_string_val"/> 48 <expand macro="list_string_val" name="names"/>
51 <expand macro="list_string_san"/> 49 <expand macro="list_string_san" name="names"/>
52 </param> 50 </param>
53 <param name="mapping" argument="-mapping" type="data" format="csv" optional="false" label="The mapping of the exported table's headers to the according qp cvs" help="The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported select csv data sets(s)"/> 51 <param argument="-mapping" type="data" format="csv" optional="false" label="The mapping of the exported table's headers to the according qp cvs" help="The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported select csv 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_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"/> 63 <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"/>
66 <data name="ctd_out" format="xml" label="${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-->
71 <expand macro="autotest_QCExporter"/> 69 </tests>
72 <expand macro="manutest_QCExporter"/>
73 </tests>
74 <help><![CDATA[Will extract several qp from several run/sets in a tabular format. 70 <help><![CDATA[Will extract several qp from several run/sets in a tabular format.
75 71
76 72
77 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_QCExporter.html]]></help> 73 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCExporter.html]]></help>
78 <expand macro="references"/> 74 <expand macro="references"/>
79 </tool> 75 </tool>