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comparison PeakPickerIterative.xml @ 14:025261d4bd60 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 21:32:08 +0000
parents 9547baeca6a1
children
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13:9547baeca6a1 14:025261d4bd60
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: Centroiding]-->
4 <tool id="PeakPickerIterative" name="PeakPickerIterative" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="PeakPickerIterative" name="PeakPickerIterative" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Finds mass spectrometric peaks in profile mass spectra.</description> 4 <description>Finds mass spectrometric peaks in profile mass spectra</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">PeakPickerIterative</token> 6 <token name="@EXECUTABLE@">PeakPickerIterative</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 parameters section" help="" expanded="false"> 42 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
44 <param name="signal_to_noise_" argument="-algorithm:signal_to_noise_" type="float" optional="true" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help=""/> 43 <param name="signal_to_noise_" argument="-algorithm:signal_to_noise_" type="float" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help=""/>
45 <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/> 44 <param name="peak_width" argument="-algorithm:peak_width" type="float" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
46 <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" optional="true" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue" help="The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak"/> 45 <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue" help="The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak"/>
47 <param name="sn_bin_count_" argument="-algorithm:sn_bin_count_" type="integer" optional="true" value="30" label="Bin count for the Signal to Noise estimation" help=""/> 46 <param name="sn_bin_count_" argument="-algorithm:sn_bin_count_" type="integer" value="30" label="Bin count for the Signal to Noise estimation" help=""/>
48 <param name="nr_iterations_" argument="-algorithm:nr_iterations_" type="integer" optional="true" min="1" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)" help=""/> 47 <param name="nr_iterations_" argument="-algorithm:nr_iterations_" type="integer" min="1" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)" help=""/>
49 <param name="sn_win_len_" argument="-algorithm:sn_win_len_" type="float" optional="true" value="20.0" label="Window length for the Signal to Noise estimation" help=""/> 48 <param name="sn_win_len_" argument="-algorithm:sn_win_len_" type="float" value="20.0" label="Window length for the Signal to Noise estimation" help=""/>
50 <param name="check_width_internally" argument="-algorithm:check_width_internally" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)" help=""/> 49 <param name="check_width_internally" argument="-algorithm:check_width_internally" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)" help=""/>
51 <param name="ms1_only" argument="-algorithm:ms1_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only do MS1" help=""/> 50 <param name="ms1_only" argument="-algorithm:ms1_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only do MS1" help=""/>
52 <param name="clear_meta_data" argument="-algorithm:clear_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete meta data about peak width" help=""/> 51 <param name="clear_meta_data" argument="-algorithm:clear_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete meta data about peak width" help=""/>
53 </section> 52 </section>
54 <expand macro="adv_opts_macro"> 53 <expand macro="adv_opts_macro">
55 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
56 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 55 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
57 <expand macro="list_string_san" name="test"/> 56 <expand macro="list_string_san" name="test"/>
58 </param> 57 </param>
59 </expand> 58 </expand>
60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
65 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 64 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
68 </data> 67 </data>
69 </outputs> 68 </outputs>
70 <tests><!-- UTILS_PeakPickerIterative_1 --> 69 <tests>
70 <!-- TOPP_PeakPickerIterative_1 -->
71 <test expect_num_outputs="2"> 71 <test expect_num_outputs="2">
72 <section name="adv_opts"> 72 <section name="adv_opts">
73 <param name="force" value="false"/> 73 <param name="force" value="false"/>
74 <param name="test" value="true"/> 74 <param name="test" value="true"/>
75 </section> 75 </section>
76 <param name="in" value="PeakPickerIterative_1_input.mzML"/> 76 <param name="in" value="PeakPickerIterative_1_input.mzML"/>
77 <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 77 <output name="out" value="PeakPickerIterative_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
78 <section name="algorithm"> 78 <section name="algorithm">
79 <param name="signal_to_noise_" value="1.0"/> 79 <param name="signal_to_noise_" value="1.0"/>
80 <param name="peak_width" value="0.04"/> 80 <param name="peak_width" value="0.04"/>
81 <param name="spacing_difference" value="1.5"/> 81 <param name="spacing_difference" value="1.5"/>
82 <param name="sn_bin_count_" value="30"/> 82 <param name="sn_bin_count_" value="30"/>
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 <!-- UTILS_PeakPickerIterative_2 --> 99 <!-- TOPP_PeakPickerIterative_2 -->
97 <test expect_num_outputs="2"> 100 <test expect_num_outputs="2">
98 <section name="adv_opts"> 101 <section name="adv_opts">
99 <param name="force" value="false"/> 102 <param name="force" value="false"/>
100 <param name="test" value="true"/> 103 <param name="test" value="true"/>
101 </section> 104 </section>
102 <param name="in" value="PeakPickerIterative_2_input.mzML"/> 105 <param name="in" value="PeakPickerIterative_2_input.mzML"/>
103 <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 106 <output name="out" value="PeakPickerIterative_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
104 <section name="algorithm"> 107 <section name="algorithm">
105 <param name="signal_to_noise_" value="0.0"/> 108 <param name="signal_to_noise_" value="0.0"/>
106 <param name="peak_width" value="0.04"/> 109 <param name="peak_width" value="0.04"/>
107 <param name="spacing_difference" value="2.5"/> 110 <param name="spacing_difference" value="2.5"/>
108 <param name="sn_bin_count_" value="30"/> 111 <param name="sn_bin_count_" value="30"/>
116 <output name="ctd_out" ftype="xml"> 119 <output name="ctd_out" ftype="xml">
117 <assert_contents> 120 <assert_contents>
118 <is_valid_xml/> 121 <is_valid_xml/>
119 </assert_contents> 122 </assert_contents>
120 </output> 123 </output>
124 <assert_stdout>
125 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
126 </assert_stdout>
121 </test> 127 </test>
122 </tests> 128 </tests>
123 <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra. 129 <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra.
124 130
125 131
126 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_PeakPickerIterative.html]]></help> 132 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PeakPickerIterative.html]]></help>
127 <expand macro="references"/> 133 <expand macro="references"/>
128 </tool> 134 </tool>