Mercurial > repos > galaxyp > openms_featurelinkerlabeled

comparison FeatureLinkerLabeled.xml @ 15:d9ebdc2e55fe draft

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 19:09:37 +0000
parents a33857ab19d0
children 90a5563d9a69
comparison
equal deleted inserted replaced
14:c781ee2e5e98 15:d9ebdc2e55fe
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="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Groups corresponding isotope-labeled features in a feature map.</description> 5 <description>Groups corresponding isotope-labeled features in a feature map.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureLinkerLabeled</token> 7 <token name="@EXECUTABLE@">FeatureLinkerLabeled</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="featurexml" optional="false" label="Input file" help=" select featurexml data sets(s)"/> 42 <param argument="-in" type="data" format="featurexml" optional="false" label="Input file" help=" select featurexml data sets(s)"/>
45 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 43 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
46 <param name="rt_estimate" argument="-algorithm:rt_estimate" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" help="Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance"/> 44 <param name="rt_estimate" argument="-algorithm:rt_estimate" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" help="Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance"/>
47 <param name="rt_pair_dist" argument="-algorithm:rt_pair_dist" type="float" optional="true" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help=""/> 45 <param name="rt_pair_dist" argument="-algorithm:rt_pair_dist" type="float" optional="true" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help=""/>
48 <param name="rt_dev_low" argument="-algorithm:rt_dev_low" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation below optimal retention time distance" help=""/> 46 <param name="rt_dev_low" argument="-algorithm:rt_dev_low" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation below optimal retention time distance" help=""/>
49 <param name="rt_dev_high" argument="-algorithm:rt_dev_high" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation above optimal retention time distance" help=""/> 47 <param name="rt_dev_high" argument="-algorithm:rt_dev_high" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation above optimal retention time distance" help=""/>
50 <param name="mz_pair_dists" argument="-algorithm:mz_pair_dists" type="text" optional="true" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3" help="by division through charge) (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 48 <param name="mz_pair_dists" argument="-algorithm:mz_pair_dists" type="text" optional="true" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3" help="by division through charge) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
51 <expand macro="list_float_valsan"/> 49 <expand macro="list_float_valsan" name="mz_pair_dists"/>
52 </param> 50 </param>
53 <param name="mz_dev" argument="-algorithm:mz_dev" type="float" optional="true" min="0.0" value="0.05" label="maximum allowed deviation from optimal m/z distance" help=""/> 51 <param name="mz_dev" argument="-algorithm:mz_dev" type="float" optional="true" min="0.0" value="0.05" label="maximum allowed deviation from optimal m/z distance" help=""/>
54 <param name="mrm" argument="-algorithm:mrm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help=""/> 52 <param name="mrm" argument="-algorithm:mrm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help=""/>
55 </section> 53 </section>
56 <expand macro="adv_opts_macro"> 54 <expand macro="adv_opts_macro">
57 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 55 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
58 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 56 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
59 <expand macro="list_string_san"/> 57 <expand macro="list_string_san" name="test"/>
60 </param> 58 </param>
61 </expand> 59 </expand>
62 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
63 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
64 </param> 62 </param>
67 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> 65 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
68 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
69 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
70 </data> 68 </data>
71 </outputs> 69 </outputs>
72 <tests> 70 <tests><!-- TOPP_FeatureLinkerLabeled_1 -->
73 <expand macro="autotest_FeatureLinkerLabeled"/> 71 <test expect_num_outputs="2">
74 <expand macro="manutest_FeatureLinkerLabeled"/> 72 <section name="adv_opts">
73 <param name="force" value="false"/>
74 <param name="test" value="true"/>
75 </section>
76 <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
77 <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
78 <section name="algorithm">
79 <param name="rt_estimate" value="false"/>
80 <param name="rt_pair_dist" value="-1.0"/>
81 <param name="rt_dev_low" value="0.4"/>
82 <param name="rt_dev_high" value="0.4"/>
83 <param name="mz_pair_dists" value="8.0"/>
84 <param name="mz_dev" value="0.1"/>
85 <param name="mrm" value="false"/>
86 </section>
87 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
88 <output name="ctd_out" ftype="xml">
89 <assert_contents>
90 <is_valid_xml/>
91 </assert_contents>
92 </output>
93 </test>
94 <!-- TOPP_FeatureLinkerLabeled_2 -->
95 <test expect_num_outputs="2">
96 <section name="adv_opts">
97 <param name="force" value="false"/>
98 <param name="test" value="true"/>
99 </section>
100 <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/>
101 <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
102 <section name="algorithm">
103 <param name="rt_estimate" value="true"/>
104 <param name="rt_pair_dist" value="-121.0382"/>
105 <param name="rt_dev_low" value="123.3965"/>
106 <param name="rt_dev_high" value="123.3965"/>
107 <param name="mz_pair_dists" value="4.0"/>
108 <param name="mz_dev" value="0.1"/>
109 <param name="mrm" value="false"/>
110 </section>
111 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
112 <output name="ctd_out" ftype="xml">
113 <assert_contents>
114 <is_valid_xml/>
115 </assert_contents>
116 </output>
117 </test>
75 </tests> 118 </tests>
76 <help><![CDATA[Groups corresponding isotope-labeled features in a feature map. 119 <help><![CDATA[Groups corresponding isotope-labeled features in a feature map.
77 120
78 121
79 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureLinkerLabeled.html]]></help> 122 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureLinkerLabeled.html]]></help>
80 <expand macro="references"/> 123 <expand macro="references"/>
81 </tool> 124 </tool>