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comparison ConsensusMapNormalizer.xml @ 17:d9802c463a2f 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 19:07:18 +0000
parents 226f58ac71c5
children
comparison
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16:3c7ace918122 17:d9802c463a2f
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: [Map Alignment]--> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Normalizes maps of one consensusXML file</description> 5 <description>Normalizes maps of one consensusXML file</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ConsensusMapNormalizer</token> 7 <token name="@EXECUTABLE@">ConsensusMapNormalizer</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@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <inputs>
44 <param name="in" argument="-in" type="data" format="consensusxml" optional="false" label="input file" help=" select consensusxml data sets(s)"/> 42 <param argument="-in" type="data" format="consensusxml" optional="false" label="input file" help=" select consensusxml data sets(s)"/>
45 <param name="algorithm_type" argument="-algorithm_type" display="radio" type="select" optional="false" label="The normalization algorithm that is applied" help="'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)"> 43 <param argument="-algorithm_type" type="select" optional="true" label="The normalization algorithm that is applied" help="'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)">
46 <option value="robust_regression" selected="true">robust_regression</option> 44 <option value="robust_regression" selected="true">robust_regression</option>
47 <option value="median">median</option> 45 <option value="median">median</option>
48 <option value="median_shift">median_shift</option> 46 <option value="median_shift">median_shift</option>
49 <option value="quantile">quantile</option> 47 <option value="quantile">quantile</option>
50 <expand macro="list_string_san"/> 48 <expand macro="list_string_san" name="algorithm_type"/>
51 </param> 49 </param>
52 <param name="ratio_threshold" argument="-ratio_threshold" type="float" optional="true" min="0.001" max="1.0" value="0.67" label="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold &lt; intensity ratio &lt; 1/ratio_threshold) and outliers" help=""/> 50 <param argument="-ratio_threshold" type="float" optional="true" min="0.001" max="1.0" value="0.67" label="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold &lt; intensity ratio &lt; 1/ratio_threshold) and outliers" help=""/>
53 <expand macro="adv_opts_macro"> 51 <expand macro="adv_opts_macro">
54 <param name="accession_filter" argument="-accession_filter" type="text" optional="true" value="" label="Use only features with accessions (partially) matching this regular expression for computing the normalization factors" help="Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used"> 52 <param argument="-accession_filter" type="text" optional="true" value="" label="Use only features with accessions (partially) matching this regular expression for computing the normalization factors" help="Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used">
55 <expand macro="list_string_san"/> 53 <expand macro="list_string_san" name="accession_filter"/>
56 </param> 54 </param>
57 <param name="description_filter" argument="-description_filter" type="text" optional="true" value="" label="Use only features with description (partially) matching this regular expression for computing the normalization factors" help="Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used"> 55 <param argument="-description_filter" type="text" optional="true" value="" label="Use only features with description (partially) matching this regular expression for computing the normalization factors" help="Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used">
58 <expand macro="list_string_san"/> 56 <expand macro="list_string_san" name="description_filter"/>
59 </param> 57 </param>
60 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 58 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
61 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 59 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
62 <expand macro="list_string_san"/> 60 <expand macro="list_string_san" name="test"/>
63 </param> 61 </param>
64 </expand> 62 </expand>
65 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
66 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
67 </param> 65 </param>
70 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> 68 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
71 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
72 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
73 </data> 71 </data>
74 </outputs> 72 </outputs>
75 <tests> 73 <tests><!-- TOPP_ConsensusMapNormalizer_1 -->
76 <expand macro="autotest_ConsensusMapNormalizer"/> 74 <test expect_num_outputs="2">
77 <expand macro="manutest_ConsensusMapNormalizer"/> 75 <section name="adv_opts">
76 <param name="accession_filter" value=""/>
77 <param name="description_filter" value=""/>
78 <param name="force" value="false"/>
79 <param name="test" value="true"/>
80 </section>
81 <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
82 <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
83 <param name="algorithm_type" value="robust_regression"/>
84 <param name="ratio_threshold" value="0.67"/>
85 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
86 <output name="ctd_out" ftype="xml">
87 <assert_contents>
88 <is_valid_xml/>
89 </assert_contents>
90 </output>
91 </test>
78 </tests> 92 </tests>
79 <help><![CDATA[Normalizes maps of one consensusXML file 93 <help><![CDATA[Normalizes maps of one consensusXML file
80 94
81 95
82 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_ConsensusMapNormalizer.html]]></help> 96 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ConsensusMapNormalizer.html]]></help>
83 <expand macro="references"/> 97 <expand macro="references"/>
84 </tool> 98 </tool>