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comparison BaselineFilter.xml @ 18:84bd73e60367 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:37:37 +0000
parents ddbae9eb797e
children
comparison
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17:ddbae9eb797e 18:84bd73e60367
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
4 <tool id="BaselineFilter" name="BaselineFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Removes the baseline from profile spectra using a top-hat filter</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">BaselineFilter</token> 6 <token name="@EXECUTABLE@">BaselineFilter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 19
21 ## Main program call 20 ## Main program call
22 21
23 set -o pipefail && 22 set -o pipefail &&
37 <configfiles> 36 <configfiles>
38 <inputs name="args_json" data_style="paths"/> 37 <inputs name="args_json" data_style="paths"/>
39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 </configfiles> 39 </configfiles>
41 <inputs> 40 <inputs>
42 <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/> 41 <param argument="-in" type="data" format="mzml" label="input raw data file" help=" select mzml data sets(s)"/>
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=""/> 42 <param argument="-struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
44 <param argument="-struc_elem_unit" type="select" optional="true" label="Unit of 'struc_elem_length' paramete" help=""> 43 <param argument="-struc_elem_unit" type="select" label="Unit of 'struc_elem_length' paramete" help="">
45 <option value="Thomson" selected="true">Thomson</option> 44 <option value="Thomson" selected="true">Thomson</option>
46 <option value="DataPoints">DataPoints</option> 45 <option value="DataPoints">DataPoints</option>
47 <expand macro="list_string_san" name="struc_elem_unit"/> 46 <expand macro="list_string_san" name="struc_elem_unit"/>
48 </param> 47 </param>
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"> 48 <param argument="-method" type="select" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
50 <option value="identity">identity</option> 49 <option value="identity">identity</option>
51 <option value="erosion">erosion</option> 50 <option value="erosion">erosion</option>
52 <option value="dilation">dilation</option> 51 <option value="dilation">dilation</option>
53 <option value="opening">opening</option> 52 <option value="opening">opening</option>
54 <option value="closing">closing</option> 53 <option value="closing">closing</option>
59 <option value="dilation_simple">dilation_simple</option> 58 <option value="dilation_simple">dilation_simple</option>
60 <expand macro="list_string_san" name="method"/> 59 <expand macro="list_string_san" name="method"/>
61 </param> 60 </param>
62 <expand macro="adv_opts_macro"> 61 <expand macro="adv_opts_macro">
63 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 62 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
64 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 63 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
65 <expand macro="list_string_san" name="test"/> 64 <expand macro="list_string_san" name="test"/>
66 </param> 65 </param>
67 </expand> 66 </expand>
68 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 67 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
69 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 68 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
73 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 72 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
74 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 73 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
75 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 74 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
76 </data> 75 </data>
77 </outputs> 76 </outputs>
78 <tests><!-- TOPP_BaselineFilter_1 --> 77 <tests>
78 <!-- TOPP_BaselineFilter_1 -->
79 <test expect_num_outputs="2"> 79 <test expect_num_outputs="2">
80 <section name="adv_opts"> 80 <section name="adv_opts">
81 <param name="force" value="false"/> 81 <param name="force" value="false"/>
82 <param name="test" value="true"/> 82 <param name="test" value="true"/>
83 </section> 83 </section>
84 <param name="in" value="BaselineFilter_input.mzML"/> 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"/> 85 <output name="out" value="BaselineFilter_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
86 <param name="struc_elem_length" value="1.5"/> 86 <param name="struc_elem_length" value="1.5"/>
87 <param name="struc_elem_unit" value="Thomson"/> 87 <param name="struc_elem_unit" value="Thomson"/>
88 <param name="method" value="tophat"/> 88 <param name="method" value="tophat"/>
89 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 89 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
90 <output name="ctd_out" ftype="xml"> 90 <output name="ctd_out" ftype="xml">
91 <assert_contents> 91 <assert_contents>
92 <is_valid_xml/> 92 <is_valid_xml/>
93 </assert_contents> 93 </assert_contents>
94 </output> 94 </output>
95 <assert_stdout>
96 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
97 </assert_stdout>
95 </test> 98 </test>
96 </tests> 99 </tests>
97 <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter. 100 <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter.
98 101
99 102
100 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_BaselineFilter.html]]></help> 103 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_BaselineFilter.html]]></help>
101 <expand macro="references"/> 104 <expand macro="references"/>
102 </tool> 105 </tool>