Mercurial > repos > recetox > aplcms_unsupervised

annotate aplcms_macros.xml @ 0:7c80b743a2db draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
author recetox
date Sun, 18 Oct 2020 10:35:33 +0000
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7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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1 <macros>
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2 <token name="@TOOL_VERSION@">6.6.6</token>
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7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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4 <xml name="requirements">
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5 <requirements>
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6 <container type="docker">recetox/aplcms:6.6.6-recetox1</container>
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7 </requirements>
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8 </xml>
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7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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10 <xml name="inputs">
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11 <inputs>
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12 <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data"
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13 help="Mass spectrometry files for peak extraction." />
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14 <yield />
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15 </inputs>
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16 </xml>
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7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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18 <xml name="history_db">
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19 <param name="known_table" type="data" format="h5" label="known_table"
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20 help="A data table containing the known metabolite ions and previously found features. The table must contain these 18 columns: chemical_formula (optional), HMDB_ID (optional), KEGG_compound_ID (optional), neutral.mass (optional), ion.type (the ion form - optional), m.z (either theoretical or mean observed m/z value of previously found features), Number_profiles_processed (the total number of processed samples to build this database), Percent_found (the percentage of historically processed samples in which the feature appeared), mz_min (minimum observed m/z value), mz_max (maximum observed m/z value), RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time), RT_min (minimum observed retention time), RT_max (maximum observed retention time), int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." />
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21 <section name="history_db" title="Known-Table settings">
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22 <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)"
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23 help="The ppm tolerance to match identified features to known metabolites/features." />
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24 <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count"
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25 help="The minimum number of occurrences of a historically unseen (unknown) feature to add this feature into the database of known features." />
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26 </section>
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27 </xml>
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7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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29 <xml name="noise_filtering">
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30 <section name="noise_filtering" title="Noise filtering and peak detection">
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31 <param name="min_exp" type="integer" min="1" value="2"
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32 label="min_exp"
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33 help="If a feature is to be included in the final feature table, it must be present in at least this number of spectra." />
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34 <param name="min_pres" type="float" value="0.5"
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35 label="min_pres"
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36 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
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37 <param name="min_run" type="float" value="12"
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38 label="min_run"
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39 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
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40 <param name="mz_tol" type="float" value="1e-05"
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41 label="mz_tol"
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42 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6. For FTMS, 1e-5 is recommended." />
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43 <param name="baseline_correct" type="float" value="0" label="baseline_correct"
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44 help="After grouping the observations, the highest intensity in each group is found. If the highest is lower than this value, the entire group will be deleted. The default value is NA, in which case the program uses a percentile of the height of the noise groups. If given a value, the value will be used as the threshold, and baseline.correct.noise.percentile will be ignored." />
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45 <param name="baseline_correct_noise_percentile" type="float" value="0.05"
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46 label="baseline_correct_noise_percentile"
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47 help="The percentile of signal strength of those EIC that don't pass the run filter, to be used as the baseline threshold of signal strength." />
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48 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
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49 label="intensity_weighted"
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50 help="Whether to weight the local density by signal intensities in initial peak detection." />
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51 </section>
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52 </xml>
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53
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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54 <xml name="feature_detection">
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55 <section name="feature_detection" title="Feature detection">
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56 <param name="shape_model" type="select" display="radio"
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57 label="shape_model"
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58 help="The mathematical model for the shape of a peak. There are two choices - bi-Gaussian and Gaussian. When the peaks are asymmetric, the bi-Gaussian is better.">
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59 <option value="Gaussian">Gaussian</option>
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60 <option value="bi-Gaussian" selected="true">bi-Gaussian</option>
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61 </param>
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62 <param name="BIC_factor" type="float" value="2.0"
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63 label="BIC_factor"
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64 help="The factor that is multiplied on the number of parameters to modify the BIC criterion. If larger than 1, models with more peaks are penalized more." />
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65 <param name="peak_estim_method" type="select" display="radio"
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66 label="peak_estim_method"
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67 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM.">
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68 <option value="moment" selected="true">Moment</option>
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69 <option value="EM">EM</option>
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70 </param>
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71 <param name="min_bandwidth" type="float" optional="true"
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72 label="min_bandwidth (optional)"
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73 help="The minimum bandwidth to use in the kernel smoother." />
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74 <param name="max_bandwidth" type="float" optional="true"
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75 label="max_bandwidth (optional)"
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76 help="The maximum bandwidth to use in the kernel smoother." />
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77 <param name="sd_cut_min" type="float" value="0.01"
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78 label="sd_cut_min"
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79 help="The minimum standard deviation of a feature to be not eliminated." />
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80 <param name="sd_cut_max" type="float" value="500"
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81 label="sd_cut_max"
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82 help="The maximum standard deviation of a feature to be not eliminated." />
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83 <param name="sigma_ratio_lim_min" type="float" value="0.01"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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84 label="sigma_ratio_lim_min"
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85 help="The lower limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." />
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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86 <param name="sigma_ratio_lim_max" type="float" value="100"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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87 label="sigma_ratio_lim_max"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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88 help="The upper limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." />
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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89 <param name="component_eliminate" type="float" value="0.01"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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90 label="component_eliminate"
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91 help="In fitting mixture of bi-Gaussian (or Gaussian) model of an EIC, when a component accounts for a proportion of intensities less than this value, the component will be ignored." />
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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92 <param name="moment_power" type="float" value="1"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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93 label="moment_power"
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94 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." />
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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95 </section>
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96 </xml>
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97
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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98 <xml name="peak_alignment">
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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99 <section name="peak_alignment" title="Peak Alignment">
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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100 <param name="align_chr_tol" type="float" optional="true"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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101 label="align_chr_tol (optional)"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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102 help="The retention time tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data." />
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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103 <param name="align_mz_tol" type="float" optional="true"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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104 label="align_mz_tol (optional)"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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105 help="The m/z tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data. This value is expressed as the percentage of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level." />
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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106 <param name="max_align_mz_diff" type="float" value="0.01"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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107 label="max_align_mz_diff"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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108 help="As the m/z tolerance is expressed in relative terms (ppm), it may not be suitable when the m/z range is wide. This parameter limits the tolerance in absolute terms. It mostly influences feature matching in higher m/z range." />
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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109 </section>
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110 </xml>
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111
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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112 <xml name="weak_signal_recovery">
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113 <section name="weak_signal_recovery" title="Weak Signal Recovery">
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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114 <param name="recover_mz_range" type="float" optional="true"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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115 label="recover_mz_range (optional)"
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116 help="The m/z around the feature m/z to search for observations. The default value is NA, in which case 1.5 times the m/z tolerance in the aligned object will be used." />
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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117 <param name="recover_chr_range" type="float" optional="true"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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118 label="recover_chr_range (optional)"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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119 help="The retention time around the feature retention time to search for observations. The default value is NA, in which case 0.5 times the retention time tolerance in the aligned object will be used." />
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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120 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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121 label="use_observed_range"
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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122 help="If the value is true, the actual range of the observed locations of the feature in all the spectra will be used." />
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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123 <param name="recover_min_count" type="integer" value="3"
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124 label="recover_min_count"
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125 help="The minimum number of raw data points to be considered as a true feature." />
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126 </section>
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127 </xml>
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128
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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129 <token name="@GENERAL_HELP@">
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130 apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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131 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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132 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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133 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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134 please refer to http://web1.sph.emory.edu/apLCMS.
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135 </token>
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136
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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137 <xml name="citations">
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138 <citations>
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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139 <citation type="doi">10.1093/bioinformatics/btp291</citation>
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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140 <citation type="doi">10.1186/1471-2105-11-559</citation>
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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141 <citation type="doi">10.1021/pr301053d</citation>
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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142 <citation type="doi">10.1093/bioinformatics/btu430</citation>
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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143 </citations>
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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144 </xml>
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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145 </macros>