Mercurial > repos > galaxyp > openms_spectrafilterwindowmower

comparison SpectraFilterWindowMower.xml @ 14:da5c2d11fcb8 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 21:33:35 +0000
parents 2876320b80a4
children
comparison
equal deleted inserted replaced
13:2876320b80a4 14:da5c2d11fcb8
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: [Identification]--> 2 <!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
4 <tool id="SpectraFilterWindowMower" name="SpectraFilterWindowMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="SpectraFilterWindowMower" name="SpectraFilterWindowMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Applies thresholdfilter to peak spectra.</description> 4 <description>Applies thresholdfilter to peak spectra</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">SpectraFilterWindowMower</token> 6 <token name="@EXECUTABLE@">SpectraFilterWindowMower</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 file" help=" select mzml data sets(s)"/> 41 <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
43 <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false"> 42 <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
44 <param name="windowsize" argument="-algorithm:windowsize" type="float" optional="true" value="50.0" label="The size of the sliding window along the m/z axis" help=""/> 43 <param name="windowsize" argument="-algorithm:windowsize" type="float" value="50.0" label="The size of the sliding window along the m/z axis" help=""/>
45 <param name="peakcount" argument="-algorithm:peakcount" type="integer" optional="true" value="2" label="The number of peaks that should be kept" help=""/> 44 <param name="peakcount" argument="-algorithm:peakcount" type="integer" value="2" label="The number of peaks that should be kept" help=""/>
46 <param name="movetype" argument="-algorithm:movetype" type="select" optional="true" label="Whether sliding window (one peak steps) or jumping window (window size steps) should be used" help=""> 45 <param name="movetype" argument="-algorithm:movetype" type="select" label="Whether sliding window (one peak steps) or jumping window (window size steps) should be used" help="">
47 <option value="slide" selected="true">slide</option> 46 <option value="slide" selected="true">slide</option>
48 <option value="jump">jump</option> 47 <option value="jump">jump</option>
49 <expand macro="list_string_san" name="movetype"/> 48 <expand macro="list_string_san" name="movetype"/>
50 </param> 49 </param>
51 </section> 50 </section>
52 <expand macro="adv_opts_macro"> 51 <expand macro="adv_opts_macro">
53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 52 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
54 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 53 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
55 <expand macro="list_string_san" name="test"/> 54 <expand macro="list_string_san" name="test"/>
56 </param> 55 </param>
57 </expand> 56 </expand>
58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 57 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
63 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 62 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
66 </data> 65 </data>
67 </outputs> 66 </outputs>
68 <tests><!-- TOPP_SpectraFilterWindowMower_1 --> 67 <tests>
68 <!-- TOPP_SpectraFilterWindowMower_1 -->
69 <test expect_num_outputs="2"> 69 <test expect_num_outputs="2">
70 <section name="adv_opts"> 70 <section name="adv_opts">
71 <param name="force" value="false"/> 71 <param name="force" value="false"/>
72 <param name="test" value="true"/> 72 <param name="test" value="true"/>
73 </section> 73 </section>
74 <param name="in" value="SpectraFilterWindowMower_1_input.mzML"/> 74 <param name="in" value="SpectraFilterWindowMower_1_input.mzML"/>
75 <output name="out" file="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 75 <output name="out" value="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
76 <section name="algorithm"> 76 <section name="algorithm">
77 <param name="windowsize" value="50.0"/> 77 <param name="windowsize" value="50.0"/>
78 <param name="peakcount" value="2"/> 78 <param name="peakcount" value="2"/>
79 <param name="movetype" value="slide"/> 79 <param name="movetype" value="slide"/>
80 </section> 80 </section>
82 <output name="ctd_out" ftype="xml"> 82 <output name="ctd_out" ftype="xml">
83 <assert_contents> 83 <assert_contents>
84 <is_valid_xml/> 84 <is_valid_xml/>
85 </assert_contents> 85 </assert_contents>
86 </output> 86 </output>
87 <assert_stdout>
88 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
89 </assert_stdout>
87 </test> 90 </test>
88 <!-- TOPP_SpectraFilterWindowMower_2 --> 91 <!-- TOPP_SpectraFilterWindowMower_2 -->
89 <test expect_num_outputs="2"> 92 <test expect_num_outputs="2">
90 <section name="adv_opts"> 93 <section name="adv_opts">
91 <param name="force" value="false"/> 94 <param name="force" value="false"/>
92 <param name="test" value="true"/> 95 <param name="test" value="true"/>
93 </section> 96 </section>
94 <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/> 97 <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/>
95 <output name="out" file="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 98 <output name="out" value="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
96 <section name="algorithm"> 99 <section name="algorithm">
97 <param name="windowsize" value="20.0"/> 100 <param name="windowsize" value="20.0"/>
98 <param name="peakcount" value="4"/> 101 <param name="peakcount" value="4"/>
99 <param name="movetype" value="slide"/> 102 <param name="movetype" value="slide"/>
100 </section> 103 </section>
102 <output name="ctd_out" ftype="xml"> 105 <output name="ctd_out" ftype="xml">
103 <assert_contents> 106 <assert_contents>
104 <is_valid_xml/> 107 <is_valid_xml/>
105 </assert_contents> 108 </assert_contents>
106 </output> 109 </output>
110 <assert_stdout>
111 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
112 </assert_stdout>
107 </test> 113 </test>
108 </tests> 114 </tests>
109 <help><![CDATA[Applies thresholdfilter to peak spectra. 115 <help><![CDATA[Applies thresholdfilter to peak spectra.
110 116
111 117
112 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterWindowMower.html]]></help> 118 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterWindowMower.html]]></help>
113 <expand macro="references"/> 119 <expand macro="references"/>
114 </tool> 120 </tool>