Mercurial > repos > galaxyp > openms_masstraceextractor

annotate MassTraceExtractor.xml @ 13:29d893e855c6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:00:15 +0000
parents d7e537b28220
children 02e876ada338
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
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4 <tool id="MassTraceExtractor" name="MassTraceExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Detects mass traces in centroided LC-MS data.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MassTraceExtractor</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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16 ## Preprocessing
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 mkdir out &&
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21 ## Main program call
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23 set -o pipefail &&
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24 @EXECUTABLE@ -write_ctd ./ &&
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25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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27 -in
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28 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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29 -out
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30 'out/output.${out_type}'
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31
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32 ## Postprocessing
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33 && mv 'out/output.${out_type}' '$out'
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34 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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35 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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36 #end if]]></command>
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37 <configfiles>
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38 <inputs name="args_json" data_style="paths"/>
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39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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40 </configfiles>
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41 <inputs>
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42 <param argument="-in" type="data" format="mzml" optional="false" label="input centroided mzML file" help=" select mzml data sets(s)"/>
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43 <param argument="-out_type" display="radio" type="select" optional="false" label="output file type -- default: determined from file extension or content" help="">
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44 <option value="consensusXML">consensusxml</option>
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45 <option value="featureXML">featurexml</option>
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46 <expand macro="list_string_san" name="out_type"/>
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47 </param>
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48 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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49 <section name="common" title="" help="" expanded="false">
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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=""/>
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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=""/>
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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=""/>
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53 </section>
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54 <section name="mtd" title="" help="" expanded="false">
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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=""/>
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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=""/>
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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">
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58 <option value="area" selected="true">area</option>
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59 <option value="median">median</option>
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60 <option value="max_height">max_height</option>
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61 <expand macro="list_string_san" name="quant_method"/>
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62 </param>
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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">
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64 <option value="outlier" selected="true">outlier</option>
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65 <option value="sample_rate">sample_rate</option>
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66 <expand macro="list_string_san" name="trace_termination_criterion"/>
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67 </param>
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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=""/>
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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=""/>
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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=""/>
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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"/>
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72 </section>
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73 <section name="epd" title="" help="" expanded="false">
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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">
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75 <option value="off">off</option>
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76 <option value="fixed" selected="true">fixed</option>
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77 <option value="auto">auto</option>
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78 <expand macro="list_string_san" name="width_filtering"/>
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79 </param>
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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"/>
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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"/>
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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=""/>
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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=""/>
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84 </section>
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85 </section>
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86 <expand macro="adv_opts_macro">
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87 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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88 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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89 <expand macro="list_string_san" name="test"/>
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90 </param>
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91 </expand>
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92 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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93 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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94 </param>
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95 </inputs>
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96 <outputs>
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97 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml">
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98 <change_format>
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99 <when input="out_type" value="featureXML" format="featurexml"/>
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100 </change_format>
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101 </data>
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102 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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103 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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104 </data>
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105 </outputs>
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106 <tests><!-- TOPP_MassTraceExtractor_1 -->
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107 <test expect_num_outputs="2">
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108 <section name="adv_opts">
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109 <param name="force" value="false"/>
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110 <param name="test" value="true"/>
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111 </section>
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112 <param name="in" value="MassTraceExtractor_1_input.mzML"/>
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113 <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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114 <param name="out_type" value="featureXML"/>
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115 <section name="algorithm">
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116 <section name="common">
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117 <param name="noise_threshold_int" value="10.0"/>
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118 <param name="chrom_peak_snr" value="3.0"/>
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119 <param name="chrom_fwhm" value="5.0"/>
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120 </section>
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121 <section name="mtd">
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122 <param name="mass_error_ppm" value="20.0"/>
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123 <param name="reestimate_mt_sd" value="true"/>
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124 <param name="quant_method" value="area"/>
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125 <param name="trace_termination_criterion" value="outlier"/>
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126 <param name="trace_termination_outliers" value="5"/>
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127 <param name="min_sample_rate" value="0.5"/>
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128 <param name="min_trace_length" value="5.0"/>
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129 <param name="max_trace_length" value="-1.0"/>
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130 </section>
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131 <section name="epd">
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132 <param name="width_filtering" value="off"/>
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133 <param name="min_fwhm" value="3.0"/>
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134 <param name="max_fwhm" value="60.0"/>
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135 <param name="masstrace_snr_filtering" value="false"/>
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136 <param name="enabled" value="true"/>
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137 </section>
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138 </section>
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139 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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140 <output name="ctd_out" ftype="xml">
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141 <assert_contents>
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142 <is_valid_xml/>
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143 </assert_contents>
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144 </output>
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145 </test>
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146 <!-- TOPP_MassTraceExtractor_2 -->
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147 <test expect_num_outputs="2">
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148 <section name="adv_opts">
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149 <param name="force" value="false"/>
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150 <param name="test" value="true"/>
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151 </section>
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152 <param name="in" value="MassTraceExtractor_1_input.mzML"/>
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153 <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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154 <param name="out_type" value="featureXML"/>
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155 <section name="algorithm">
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156 <section name="common">
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157 <param name="noise_threshold_int" value="10.0"/>
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158 <param name="chrom_peak_snr" value="3.0"/>
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159 <param name="chrom_fwhm" value="5.0"/>
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160 </section>
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161 <section name="mtd">
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162 <param name="mass_error_ppm" value="20.0"/>
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163 <param name="reestimate_mt_sd" value="true"/>
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164 <param name="quant_method" value="area"/>
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165 <param name="trace_termination_criterion" value="outlier"/>
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166 <param name="trace_termination_outliers" value="5"/>
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167 <param name="min_sample_rate" value="0.5"/>
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168 <param name="min_trace_length" value="6.0"/>
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169 <param name="max_trace_length" value="12.0"/>
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170 </section>
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171 <section name="epd">
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172 <param name="width_filtering" value="off"/>
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173 <param name="min_fwhm" value="3.0"/>
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174 <param name="max_fwhm" value="60.0"/>
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175 <param name="masstrace_snr_filtering" value="false"/>
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176 <param name="enabled" value="true"/>
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177 </section>
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178 </section>
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179 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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180 <output name="ctd_out" ftype="xml">
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181 <assert_contents>
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182 <is_valid_xml/>
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183 </assert_contents>
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184 </output>
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185 </test>
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186 </tests>
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187 <help><![CDATA[Detects mass traces in centroided LC-MS data.
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188
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189
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190 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MassTraceExtractor.html]]></help>
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191 <expand macro="references"/>
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192 </tool>