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comparison BaselineFilter.xml @ 17:ddbae9eb797e 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 19:10:21 +0000
parents 1936361a3dbb
children
comparison
equal deleted inserted replaced
16:d46f60c75db4 17:ddbae9eb797e
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: [Signal processing and preprocessing]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="BaselineFilter" name="BaselineFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="BaselineFilter" name="BaselineFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Removes the baseline from profile spectra using a top-hat filter.</description> 5 <description>Removes the baseline from profile spectra using a top-hat filter.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">BaselineFilter</token> 7 <token name="@EXECUTABLE@">BaselineFilter</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="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/> 42 <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
45 <param name="struc_elem_length" argument="-struc_elem_length" type="float" optional="true" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/> 43 <param argument="-struc_elem_length" type="float" optional="true" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
46 <param name="struc_elem_unit" argument="-struc_elem_unit" display="radio" type="select" optional="false" label="Unit of 'struc_elem_length' paramete" help=""> 44 <param argument="-struc_elem_unit" type="select" optional="true" label="Unit of 'struc_elem_length' paramete" help="">
47 <option value="Thomson" selected="true">Thomson</option> 45 <option value="Thomson" selected="true">Thomson</option>
48 <option value="DataPoints">DataPoints</option> 46 <option value="DataPoints">DataPoints</option>
49 <expand macro="list_string_san"/> 47 <expand macro="list_string_san" name="struc_elem_unit"/>
50 </param> 48 </param>
51 <param name="method" argument="-method" type="select" optional="false" label="The name of the morphological filter to be applied" help="If you are unsure, use the default"> 49 <param argument="-method" type="select" optional="true" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
52 <option value="identity">identity</option> 50 <option value="identity">identity</option>
53 <option value="erosion">erosion</option> 51 <option value="erosion">erosion</option>
54 <option value="dilation">dilation</option> 52 <option value="dilation">dilation</option>
55 <option value="opening">opening</option> 53 <option value="opening">opening</option>
56 <option value="closing">closing</option> 54 <option value="closing">closing</option>
57 <option value="gradient">gradient</option> 55 <option value="gradient">gradient</option>
58 <option value="tophat" selected="true">tophat</option> 56 <option value="tophat" selected="true">tophat</option>
59 <option value="bothat">bothat</option> 57 <option value="bothat">bothat</option>
60 <option value="erosion_simple">erosion_simple</option> 58 <option value="erosion_simple">erosion_simple</option>
61 <option value="dilation_simple">dilation_simple</option> 59 <option value="dilation_simple">dilation_simple</option>
62 <expand macro="list_string_san"/> 60 <expand macro="list_string_san" name="method"/>
63 </param> 61 </param>
64 <expand macro="adv_opts_macro"> 62 <expand macro="adv_opts_macro">
65 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 63 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
66 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 64 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
67 <expand macro="list_string_san"/> 65 <expand macro="list_string_san" name="test"/>
68 </param> 66 </param>
69 </expand> 67 </expand>
70 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 68 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
71 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 69 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
72 </param> 70 </param>
75 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 73 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
76 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 74 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
77 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 75 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
78 </data> 76 </data>
79 </outputs> 77 </outputs>
80 <tests> 78 <tests><!-- TOPP_BaselineFilter_1 -->
81 <expand macro="autotest_BaselineFilter"/> 79 <test expect_num_outputs="2">
82 <expand macro="manutest_BaselineFilter"/> 80 <section name="adv_opts">
81 <param name="force" value="false"/>
82 <param name="test" value="true"/>
83 </section>
84 <param name="in" value="BaselineFilter_input.mzML"/>
85 <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
86 <param name="struc_elem_length" value="1.5"/>
87 <param name="struc_elem_unit" value="Thomson"/>
88 <param name="method" value="tophat"/>
89 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
90 <output name="ctd_out" ftype="xml">
91 <assert_contents>
92 <is_valid_xml/>
93 </assert_contents>
94 </output>
95 </test>
83 </tests> 96 </tests>
84 <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter. 97 <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter.
85 98
86 99
87 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_BaselineFilter.html]]></help> 100 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_BaselineFilter.html]]></help>
88 <expand macro="references"/> 101 <expand macro="references"/>
89 </tool> 102 </tool>