Mercurial > repos > galaxyp > openms_ffeval

comparison FFEval.xml @ 15:71b4a047afe5 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:18:01 +0000
parents a02af506fe40
children
comparison
equal deleted inserted replaced
14:cd0102328af8 15:71b4a047afe5
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="FFEval" name="FFEval" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="FFEval" name="FFEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Evaluation tool for feature detection algorithms.</description> 5 <description>Evaluation tool for feature detection algorithms.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FFEval</token> 7 <token name="@EXECUTABLE@">FFEval</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@
70 <configfiles> 68 <configfiles>
71 <inputs name="args_json" data_style="paths"/> 69 <inputs name="args_json" data_style="paths"/>
72 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 70 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
73 </configfiles> 71 </configfiles>
74 <inputs> 72 <inputs>
75 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Feature input file, which contains the data to be tested against the truth file" help=" select featurexml data sets(s)"/> 73 <param argument="-in" type="data" format="featurexml" optional="false" label="Feature input file, which contains the data to be tested against the truth file" help=" select featurexml data sets(s)"/>
76 <param name="truth" argument="-truth" type="data" format="featurexml" optional="false" label="Truth feature file that defines what features should be found" help=" select featurexml data sets(s)"/> 74 <param argument="-truth" type="data" format="featurexml" optional="false" label="Truth feature file that defines what features should be found" help=" select featurexml data sets(s)"/>
77 <param name="rt_tol" argument="-rt_tol" type="float" optional="true" min="0.0" value="0.3" label="Allowed tolerance of RT relative to average feature RT span" help=""/> 75 <param argument="-rt_tol" type="float" optional="true" min="0.0" value="0.3" label="Allowed tolerance of RT relative to average feature RT span" help=""/>
78 <param name="rt_tol_abs" argument="-rt_tol_abs" type="float" optional="true" min="-1.0" value="-1.0" label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" help=""/> 76 <param argument="-rt_tol_abs" type="float" optional="true" min="-1.0" value="-1.0" label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" help=""/>
79 <param name="mz_tol" argument="-mz_tol" type="float" optional="true" min="0.0" value="0.25" label="Allowed tolerance in m/z (is divided by charge)" help=""/> 77 <param argument="-mz_tol" type="float" optional="true" min="0.0" value="0.25" label="Allowed tolerance in m/z (is divided by charge)" help=""/>
80 <param name="abort_reasons" argument="-abort_reasons" type="data" format="featurexml" optional="true" label="Feature file containing seeds with abort reasons" help=" select featurexml data sets(s)"/> 78 <param argument="-abort_reasons" type="data" format="featurexml" optional="true" label="Feature file containing seeds with abort reasons" help=" select featurexml data sets(s)"/>
81 <expand macro="adv_opts_macro"> 79 <expand macro="adv_opts_macro">
82 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 80 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
83 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 81 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
84 <expand macro="list_string_san"/> 82 <expand macro="list_string_san" name="test"/>
85 </param> 83 </param>
86 </expand> 84 </expand>
87 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 85 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
88 <option value="out_FLAG">out (Feature output file)</option> 86 <option value="out_FLAG">out (Feature output file)</option>
89 <option value="out_roc_FLAG">out_roc (If given, a ROC curve file is created (ROC points based on intensity threshold))</option> 87 <option value="out_roc_FLAG">out_roc (If given, a ROC curve file is created (ROC points based on intensity threshold))</option>
102 </data> 100 </data>
103 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 101 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
104 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 102 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
105 </data> 103 </data>
106 </outputs> 104 </outputs>
107 <tests> 105 <tests><test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself -->
108 <expand macro="autotest_FFEval"/> 106 <param name="adv_opts|test" value="true"/>
109 <expand macro="manutest_FFEval"/> 107 <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/>
110 </tests> 108 <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/>
109 <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/>
110 <output name="out" value="FFEval.featureXML" compare="sim_size"/>
111 <output name="out_roc" value="FFEval_roc.csv" ftype="csv"/>
112 </test>
113 </tests>
111 <help><![CDATA[Evaluation tool for feature detection algorithms. 114 <help><![CDATA[Evaluation tool for feature detection algorithms.
112 115
113 116
114 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_FFEval.html]]></help> 117 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FFEval.html]]></help>
115 <expand macro="references"/> 118 <expand macro="references"/>
116 </tool> 119 </tool>