Mercurial > repos > galaxyp > openms_masstraceextractor

comparison MassTraceExtractor.xml @ 9:5d7b3d2b66a8 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:38:30 -0400
parents e059a211406b
children d7e537b28220
comparison
equal deleted inserted replaced
8:dde27d8dd501 9:5d7b3d2b66a8
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="MassTraceExtractor" name="MassTraceExtractor" version="2.3.0"> 4 <tool id="MassTraceExtractor" name="MassTraceExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Detects mass traces in centroided LC-MS data.</description> 5 <description>Detects mass traces in centroided LC-MS data.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MassTraceExtractor</token> 7 <token name="@EXECUTABLE@">MassTraceExtractor</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[MassTraceExtractor 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21 mkdir out &&
19 -out $param_out 22
20 #end if 23 ## Main program call
21 #if $param_out_type: 24
22 -out_type 25 set -o pipefail &&
23 #if " " in str($param_out_type): 26 @EXECUTABLE@ -write_ctd ./ &&
24 "$param_out_type" 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 #else 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 $param_out_type 29 -in
27 #end if 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 #end if 31 -out
29 #if $param_algorithm_common_noise_threshold_int: 32 'out/output.${out_type}'
30 -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int 33
31 #end if 34 ## Postprocessing
32 #if $param_algorithm_common_chrom_peak_snr: 35 && mv 'out/output.${out_type}' '$out'
33 -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 #end if 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 #if $param_algorithm_common_chrom_fwhm: 38 #end if]]></command>
36 -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm 39 <configfiles>
37 #end if 40 <inputs name="args_json" data_style="paths"/>
38 #if $param_algorithm_mtd_mass_error_ppm: 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm 42 </configfiles>
40 #end if
41 #if $param_algorithm_mtd_reestimate_mt_sd:
42 -algorithm:mtd:reestimate_mt_sd
43 #if " " in str($param_algorithm_mtd_reestimate_mt_sd):
44 "$param_algorithm_mtd_reestimate_mt_sd"
45 #else
46 $param_algorithm_mtd_reestimate_mt_sd
47 #end if
48 #end if
49 #if $param_algorithm_mtd_quant_method:
50 -algorithm:mtd:quant_method
51 #if " " in str($param_algorithm_mtd_quant_method):
52 "$param_algorithm_mtd_quant_method"
53 #else
54 $param_algorithm_mtd_quant_method
55 #end if
56 #end if
57 #if $param_algorithm_epd_width_filtering:
58 -algorithm:epd:width_filtering
59 #if " " in str($param_algorithm_epd_width_filtering):
60 "$param_algorithm_epd_width_filtering"
61 #else
62 $param_algorithm_epd_width_filtering
63 #end if
64 #end if
65 #if $param_algorithm_epd_enabled:
66 -algorithm:epd:enabled
67 #if " " in str($param_algorithm_epd_enabled):
68 "$param_algorithm_epd_enabled"
69 #else
70 $param_algorithm_epd_enabled
71 #end if
72 #end if
73 #if $adv_opts.adv_opts_selector=='advanced':
74 #if $adv_opts.param_force:
75 -force
76 #end if
77 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
78 -algorithm:mtd:trace_termination_criterion
79 #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
80 "$adv_opts.param_algorithm_mtd_trace_termination_criterion"
81 #else
82 $adv_opts.param_algorithm_mtd_trace_termination_criterion
83 #end if
84 #end if
85 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
86 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
87 #end if
88 #if $adv_opts.param_algorithm_mtd_min_sample_rate:
89 -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate
90 #end if
91 #if $adv_opts.param_algorithm_mtd_min_trace_length:
92 -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length
93 #end if
94 #if $adv_opts.param_algorithm_mtd_max_trace_length:
95 -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length
96 #end if
97 #if $adv_opts.param_algorithm_epd_min_fwhm:
98 -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm
99 #end if
100 #if $adv_opts.param_algorithm_epd_max_fwhm:
101 -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm
102 #end if
103 #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering:
104 -algorithm:epd:masstrace_snr_filtering
105 #end if
106 #end if
107 ]]></command>
108 <inputs> 43 <inputs>
109 <param name="param_in" type="data" format="mzml" optional="False" label="input centroided mzML file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input centroided mzML file" help=" select mzml data sets(s)"/>
110 <param name="param_out_type" display="radio" type="select" optional="True" label="output file type -- default: determined from file extension or content" help="(-out_type) "> 45 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="output file type -- default: determined from file extension or content" help="">
111 <option value="featureXML">featureXML</option> 46 <option value="consensusXML">consensusxml</option>
112 <option value="consensusXML">consensusXML</option> 47 <option value="featureXML">featurexml</option>
48 <expand macro="list_string_san"/>
113 </param> 49 </param>
114 <param name="param_algorithm_common_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help="(-noise_threshold_int) "/> 50 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
115 <param name="param_algorithm_common_chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help="(-chrom_peak_snr) "/> 51 <section name="common" title="" help="" expanded="false">
116 <param name="param_algorithm_common_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help="(-chrom_fwhm) "/> 52 <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=""/>
117 <param name="param_algorithm_mtd_mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)" help="(-mass_error_ppm) "/> 53 <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=""/>
118 <param name="param_algorithm_mtd_reestimate_mt_sd" display="radio" type="select" optional="False" value="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help="(-reestimate_mt_sd) "> 54 <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" optional="true" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/>
119 <option value="true" selected="true">true</option> 55 </section>
120 <option value="false">false</option> 56 <section name="mtd" title="" help="" expanded="false">
57 <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=""/>
58 <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=""/>
59 <param name="quant_method" argument="-algorithm:mtd:quant_method" display="radio" type="select" optional="false" 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">
60 <option value="area" selected="true">area</option>
61 <option value="median">median</option>
62 <option value="max_height">max_height</option>
63 <expand macro="list_string_san"/>
64 </param>
65 <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" display="radio" type="select" optional="false" 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">
66 <option value="outlier" selected="true">outlier</option>
67 <option value="sample_rate">sample_rate</option>
68 <expand macro="list_string_san"/>
69 </param>
70 <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=""/>
71 <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=""/>
72 <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=""/>
73 <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"/>
74 </section>
75 <section name="epd" title="" help="" expanded="false">
76 <param name="width_filtering" argument="-algorithm:epd:width_filtering" display="radio" type="select" optional="false" 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">
77 <option value="off">off</option>
78 <option value="fixed" selected="true">fixed</option>
79 <option value="auto">auto</option>
80 <expand macro="list_string_san"/>
81 </param>
82 <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="3.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
83 <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"/>
84 <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=""/>
85 <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=""/>
86 </section>
87 </section>
88 <expand macro="adv_opts_macro">
89 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
90 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
91 <expand macro="list_string_san"/>
92 </param>
93 </expand>
94 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
95 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
121 </param> 96 </param>
122 <param name="param_algorithm_mtd_quant_method" display="radio" type="select" optional="False" value="area" label="Method of quantification for mass traces" help="(-quant_method) For LC data 'area' is recommended, 'median' for direct injection data">
123 <option value="area" selected="true">area</option>
124 <option value="median">median</option>
125 </param>
126 <param name="param_algorithm_epd_width_filtering" display="radio" type="select" optional="False" value="fixed" label="Enable filtering of unlikely peak widths" help="(-width_filtering) 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">
127 <option value="off">off</option>
128 <option value="fixed" selected="true">fixed</option>
129 <option value="auto">auto</option>
130 </param>
131 <param name="param_algorithm_epd_enabled" display="radio" type="select" optional="False" value="true" label="Enables/disables the chromatographic peak detection of mass traces" help="(-enabled) ">
132 <option value="true" selected="true">true</option>
133 <option value="false">false</option>
134 </param>
135 <expand macro="advanced_options">
136 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
137 <param name="param_algorithm_mtd_trace_termination_criterion" display="radio" type="select" optional="False" value="outlier" label="Termination criterion for the extension of mass traces" help="(-trace_termination_criterion) 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">
138 <option value="outlier" selected="true">outlier</option>
139 <option value="sample_rate">sample_rate</option>
140 </param>
141 <param name="param_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="(-trace_termination_outliers) "/>
142 <param name="param_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="(-min_sample_rate) "/>
143 <param name="param_algorithm_mtd_min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help="(-min_trace_length) "/>
144 <param name="param_algorithm_mtd_max_trace_length" type="float" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="(-max_trace_length) Set to a negative value to disable maximal length check during mass trace detection"/>
145 <param name="param_algorithm_epd_min_fwhm" type="float" value="3.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="(-min_fwhm) Ignored if parameter width_filtering is off or auto"/>
146 <param name="param_algorithm_epd_max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="(-max_fwhm) Ignored if parameter width_filtering is off or auto"/>
147 <param name="param_algorithm_epd_masstrace_snr_filtering" display="radio" type="boolean" truevalue="-algorithm:epd:masstrace_snr_filtering" falsevalue="" checked="false" optional="True" label="Apply post-filtering by signal-to-noise ratio after smoothing" help="(-masstrace_snr_filtering) "/>
148 </expand>
149 </inputs> 97 </inputs>
150 <outputs> 98 <outputs>
151 <data name="param_out" format="featurexml"/> 99 <data name="out" label="${tool.name} on ${on_string}: out">
100 <change_format>
101 <when input="out_type" value="consensusXML" format="consensusxml"/>
102 <when input="out_type" value="featureXML" format="featurexml"/>
103 </change_format>
104 </data>
105 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
106 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
107 </data>
152 </outputs> 108 </outputs>
153 <help>Detects mass traces in centroided LC-MS data. 109 <tests>
110 <expand macro="autotest_MassTraceExtractor"/>
111 <expand macro="manutest_MassTraceExtractor"/>
112 </tests>
113 <help><![CDATA[Detects mass traces in centroided LC-MS data.
154 114
155 115
156 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MassTraceExtractor.html</help> 116 For more information, visit http://www.openms.de/documentation/TOPP_MassTraceExtractor.html]]></help>
117 <expand macro="references"/>
157 </tool> 118 </tool>