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comparison MassTraceExtractor.xml @ 14:02e876ada338 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 21:27:39 +0000
parents 29d893e855c6
children
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13:29d893e855c6 14:02e876ada338
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: [Quantitation]-->
4 <tool id="MassTraceExtractor" name="MassTraceExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="MassTraceExtractor" name="MassTraceExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Detects mass traces in centroided LC-MS data.</description> 4 <description>Detects mass traces in centroided LC-MS data</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">MassTraceExtractor</token> 6 <token name="@EXECUTABLE@">MassTraceExtractor</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 centroided mzML file" help=" select mzml data sets(s)"/> 41 <param argument="-in" type="data" format="mzml" label="input centroided mzML file" help=" select mzml data sets(s)"/>
43 <param argument="-out_type" display="radio" type="select" optional="false" label="output file type -- default: determined from file extension or content" help=""> 42 <param argument="-out_type" type="select" label="output file type -- default: determined from file extension or content" help="">
44 <option value="consensusXML">consensusxml</option> 43 <option value="consensusXML">consensusxml</option>
45 <option value="featureXML">featurexml</option> 44 <option value="featureXML">featurexml</option>
45 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
46 <expand macro="list_string_san" name="out_type"/> 46 <expand macro="list_string_san" name="out_type"/>
47 </param> 47 </param>
48 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 48 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
49 <section name="common" title="" help="" expanded="false"> 49 <section name="common" title="" help="" expanded="false">
50 <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" optional="true" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/> 50 <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/>
51 <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" optional="true" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/> 51 <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/>
52 <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" optional="true" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/> 52 <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/>
53 </section> 53 </section>
54 <section name="mtd" title="" help="" expanded="false"> 54 <section name="mtd" title="" help="" expanded="false">
55 <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" optional="true" value="20.0" label="Allowed mass deviation (in ppm)" help=""/> 55 <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
56 <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/> 56 <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/>
57 <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" optional="true" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace"> 57 <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
58 <option value="area" selected="true">area</option> 58 <option value="area" selected="true">area</option>
59 <option value="median">median</option> 59 <option value="median">median</option>
60 <option value="max_height">max_height</option> 60 <option value="max_height">max_height</option>
61 <expand macro="list_string_san" name="quant_method"/> 61 <expand macro="list_string_san" name="quant_method"/>
62 </param> 62 </param>
63 <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" optional="true" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold"> 63 <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
64 <option value="outlier" selected="true">outlier</option> 64 <option value="outlier" selected="true">outlier</option>
65 <option value="sample_rate">sample_rate</option> 65 <option value="sample_rate">sample_rate</option>
66 <expand macro="list_string_san" name="trace_termination_criterion"/> 66 <expand macro="list_string_san" name="trace_termination_criterion"/>
67 </param> 67 </param>
68 <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" optional="true" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/> 68 <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/>
69 <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" optional="true" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/> 69 <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/>
70 <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" optional="true" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/> 70 <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/>
71 <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" optional="true" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/> 71 <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/>
72 </section> 72 </section>
73 <section name="epd" title="" help="" expanded="false"> 73 <section name="epd" title="" help="" expanded="false">
74 <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" optional="true" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution"> 74 <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
75 <option value="off">off</option> 75 <option value="off">off</option>
76 <option value="fixed" selected="true">fixed</option> 76 <option value="fixed" selected="true">fixed</option>
77 <option value="auto">auto</option> 77 <option value="auto">auto</option>
78 <expand macro="list_string_san" name="width_filtering"/> 78 <expand macro="list_string_san" name="width_filtering"/>
79 </param> 79 </param>
80 <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/> 80 <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
81 <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" optional="true" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/> 81 <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
82 <param name="masstrace_snr_filtering" argument="-algorithm:epd:masstrace_snr_filtering" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply post-filtering by signal-to-noise ratio after smoothing" help=""/> 82 <param name="masstrace_snr_filtering" argument="-algorithm:epd:masstrace_snr_filtering" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply post-filtering by signal-to-noise ratio after smoothing" help=""/>
83 <param name="enabled" argument="-algorithm:epd:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables/disables the chromatographic peak detection of mass traces" help=""/> 83 <param name="enabled" argument="-algorithm:epd:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables/disables the chromatographic peak detection of mass traces" help=""/>
84 </section> 84 </section>
85 </section> 85 </section>
86 <expand macro="adv_opts_macro"> 86 <expand macro="adv_opts_macro">
87 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 87 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
88 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 88 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
89 <expand macro="list_string_san" name="test"/> 89 <expand macro="list_string_san" name="test"/>
90 </param> 90 </param>
91 </expand> 91 </expand>
92 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 92 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
93 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 93 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
101 </data> 101 </data>
102 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 102 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
103 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 103 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
104 </data> 104 </data>
105 </outputs> 105 </outputs>
106 <tests><!-- TOPP_MassTraceExtractor_1 --> 106 <tests>
107 <!-- TOPP_MassTraceExtractor_1 -->
107 <test expect_num_outputs="2"> 108 <test expect_num_outputs="2">
108 <section name="adv_opts"> 109 <section name="adv_opts">
109 <param name="force" value="false"/> 110 <param name="force" value="false"/>
110 <param name="test" value="true"/> 111 <param name="test" value="true"/>
111 </section> 112 </section>
112 <param name="in" value="MassTraceExtractor_1_input.mzML"/> 113 <param name="in" value="MassTraceExtractor_1_input.mzML"/>
113 <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 114 <output name="out" value="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
114 <param name="out_type" value="featureXML"/> 115 <param name="out_type" value="featureXML"/>
115 <section name="algorithm"> 116 <section name="algorithm">
116 <section name="common"> 117 <section name="common">
117 <param name="noise_threshold_int" value="10.0"/> 118 <param name="noise_threshold_int" value="10.0"/>
118 <param name="chrom_peak_snr" value="3.0"/> 119 <param name="chrom_peak_snr" value="3.0"/>
140 <output name="ctd_out" ftype="xml"> 141 <output name="ctd_out" ftype="xml">
141 <assert_contents> 142 <assert_contents>
142 <is_valid_xml/> 143 <is_valid_xml/>
143 </assert_contents> 144 </assert_contents>
144 </output> 145 </output>
146 <assert_stdout>
147 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
148 </assert_stdout>
145 </test> 149 </test>
146 <!-- TOPP_MassTraceExtractor_2 --> 150 <!-- TOPP_MassTraceExtractor_2 -->
147 <test expect_num_outputs="2"> 151 <test expect_num_outputs="2">
148 <section name="adv_opts"> 152 <section name="adv_opts">
149 <param name="force" value="false"/> 153 <param name="force" value="false"/>
150 <param name="test" value="true"/> 154 <param name="test" value="true"/>
151 </section> 155 </section>
152 <param name="in" value="MassTraceExtractor_1_input.mzML"/> 156 <param name="in" value="MassTraceExtractor_1_input.mzML"/>
153 <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 157 <output name="out" value="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
154 <param name="out_type" value="featureXML"/> 158 <param name="out_type" value="featureXML"/>
155 <section name="algorithm"> 159 <section name="algorithm">
156 <section name="common"> 160 <section name="common">
157 <param name="noise_threshold_int" value="10.0"/> 161 <param name="noise_threshold_int" value="10.0"/>
158 <param name="chrom_peak_snr" value="3.0"/> 162 <param name="chrom_peak_snr" value="3.0"/>
180 <output name="ctd_out" ftype="xml"> 184 <output name="ctd_out" ftype="xml">
181 <assert_contents> 185 <assert_contents>
182 <is_valid_xml/> 186 <is_valid_xml/>
183 </assert_contents> 187 </assert_contents>
184 </output> 188 </output>
189 <assert_stdout>
190 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
191 </assert_stdout>
185 </test> 192 </test>
186 </tests> 193 </tests>
187 <help><![CDATA[Detects mass traces in centroided LC-MS data. 194 <help><![CDATA[Detects mass traces in centroided LC-MS data.
188 195
189 196
190 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MassTraceExtractor.html]]></help> 197 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MassTraceExtractor.html]]></help>
191 <expand macro="references"/> 198 <expand macro="references"/>
192 </tool> 199 </tool>