Mercurial > repos > galaxyp > openms_labeledeval

comparison LabeledEval.xml @ 13:45b7070b3366 draft default tip

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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 19:25:01 +0000
parents 01d8dbc6ccf7
children
comparison
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12:43e8e8df1af6 13:45b7070b3366
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="LabeledEval" name="LabeledEval" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="LabeledEval" name="LabeledEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description> Evaluation tool for isotope-labeled quantitation experiments.</description> 5 <description> Evaluation tool for isotope-labeled quantitation experiments.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">LabeledEval</token> 7 <token name="@EXECUTABLE@">LabeledEval</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@
40 <configfiles> 38 <configfiles>
41 <inputs name="args_json" data_style="paths"/> 39 <inputs name="args_json" data_style="paths"/>
42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 40 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
43 </configfiles> 41 </configfiles>
44 <inputs> 42 <inputs>
45 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Feature result file" help=" select featurexml data sets(s)"/> 43 <param argument="-in" type="data" format="featurexml" optional="false" label="Feature result file" help=" select featurexml data sets(s)"/>
46 <param name="truth" argument="-truth" type="data" format="consensusxml" optional="false" label="Expected result file" help=" select consensusxml data sets(s)"/> 44 <param argument="-truth" type="data" format="consensusxml" optional="false" label="Expected result file" help=" select consensusxml data sets(s)"/>
47 <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="20.0" label="Maximum allowed retention time deviation" help=""/> 45 <param argument="-rt_tol" type="float" optional="true" value="20.0" label="Maximum allowed retention time deviation" help=""/>
48 <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="0.25" label="Maximum allowed m/z deviation (divided by charge)" help=""/> 46 <param argument="-mz_tol" type="float" optional="true" value="0.25" label="Maximum allowed m/z deviation (divided by charge)" help=""/>
49 <expand macro="adv_opts_macro"> 47 <expand macro="adv_opts_macro">
50 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 48 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
51 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 49 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
52 <expand macro="list_string_san"/> 50 <expand macro="list_string_san" name="test"/>
53 </param> 51 </param>
54 </expand> 52 </expand>
55 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 53 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
56 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 54 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
57 </param> 55 </param>
62 </data> 60 </data>
63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 61 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 62 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
65 </data> 63 </data>
66 </outputs> 64 </outputs>
67 <tests> 65 <tests><test expect_num_outputs="1"><!-- comparing an arbitarty featureXML that has a corresponding consensusXML -->
68 <expand macro="autotest_LabeledEval"/> 66 <param name="adv_opts|test" value="true"/>
69 <expand macro="manutest_LabeledEval"/> 67 <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
70 </tests> 68 <param name="truth" value="FeatureLinkerLabeled_1_output.consensusXML"/>
69 <output name="stdout" value="LabeledEval.txt" compare="sim_size"/>
70 </test>
71 </tests>
71 <help><![CDATA[ Evaluation tool for isotope-labeled quantitation experiments. 72 <help><![CDATA[ Evaluation tool for isotope-labeled quantitation experiments.
72 73
73 74
74 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_LabeledEval.html]]></help> 75 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_LabeledEval.html]]></help>
75 <expand macro="references"/> 76 <expand macro="references"/>
76 </tool> 77 </tool>