Mercurial > repos > galaxyp > openms_rtevaluation

comparison RTEvaluation.xml @ 13:062fcf33f18d 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 19:21:02 +0000
parents b08e0ac606a4
children
comparison
equal deleted inserted replaced
12:9afeeb2c5b59 13:062fcf33f18d
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="RTEvaluation" name="RTEvaluation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="RTEvaluation" name="RTEvaluation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description> 5 <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">RTEvaluation</token> 7 <token name="@EXECUTABLE@">RTEvaluation</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="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/> 50 <param argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
53 <param name="sequences_file" argument="-sequences_file" type="data" format="fasta" optional="true" label="Fasta File" help=" select fasta data sets(s)"/> 51 <param argument="-sequences_file" type="data" format="fasta" optional="true" label="Fasta File" help=" select fasta data sets(s)"/>
54 <param name="latex" argument="-latex" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Indicates whether the output file format of the table should be LaTeX or TSV (default)" help=""/> 52 <param argument="-latex" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Indicates whether the output file format of the table should be LaTeX or TSV (default)" help=""/>
55 <param name="p_value_dim_1" argument="-p_value_dim_1" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Significance level of first dimension RT filte" help=""/> 53 <param argument="-p_value_dim_1" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Significance level of first dimension RT filte" help=""/>
56 <param name="p_value_dim_2" argument="-p_value_dim_2" type="float" optional="true" min="0.0" max="1.0" value="0.05" label="Significance level of second dimension RT filte" help=""/> 54 <param argument="-p_value_dim_2" type="float" optional="true" min="0.0" max="1.0" value="0.05" label="Significance level of second dimension RT filte" help=""/>
57 <expand macro="adv_opts_macro"> 55 <expand macro="adv_opts_macro">
58 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 56 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
59 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 57 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
60 <expand macro="list_string_san"/> 58 <expand macro="list_string_san" name="test"/>
61 </param> 59 </param>
62 </expand> 60 </expand>
63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 61 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
65 </param> 63 </param>
68 <data name="out" label="${tool.name} on ${on_string}: out" format="tabular"/> 66 <data name="out" label="${tool.name} on ${on_string}: out" format="tabular"/>
69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 67 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 68 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
71 </data> 69 </data>
72 </outputs> 70 </outputs>
73 <tests> 71 <tests><!-- just chosen an arbitrary input and autgenerated output-->
74 <expand macro="autotest_RTEvaluation"/> 72 <test expect_num_outputs="1">
75 <expand macro="manutest_RTEvaluation"/> 73 <param name="adv_opts|test" value="true"/>
76 </tests> 74 <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/>
75 <output name="out" ftype="tabular" value="RTEvaluation.tsv"/>
76 </test>
77 </tests>
77 <help><![CDATA[Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. 78 <help><![CDATA[Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
78 79
79 80
80 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_RTEvaluation.html]]></help> 81 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RTEvaluation.html]]></help>
81 <expand macro="references"/> 82 <expand macro="references"/>
82 </tool> 83 </tool>