Mercurial > repos > galaxyp > openms_baselinefilter
comparison BaselineFilter.xml @ 17:ddbae9eb797e draft
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 | 84bd73e60367 |
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> |