Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals

comparison macros.xml @ 8:99d118321d5f draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 0873c036d734782d2647b0eea84cd1a0658f5e58
author recetox
date Wed, 19 Jul 2023 00:27:52 +0000
parents c3d4b82c7e5d
children a9bb2ccc53de
comparison
equal deleted inserted replaced
7:c3d4b82c7e5d 8:99d118321d5f
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.11.0</token> 2 <token name="@TOOL_VERSION@">0.12.0</token>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement> 5 <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
6 <requirement type="package" version="2.5.2">pymzml</requirement> 6 <requirement type="package" version="2.5.2">pymzml</requirement>
7 </requirements> 7 </requirements>
51 name="RECETOX MUNI"/> 51 name="RECETOX MUNI"/>
52 </creator> 52 </creator>
53 </xml> 53 </xml>
54 54
55 <xml name="remove_noise_params"> 55 <xml name="remove_noise_params">
56 <param name="min_pres" type="float" value="0.5" label="Minimal signal presence [fraction of scans]" 56 <param name="min_pres" type="float" value="0.5" label="Minimal signal presence [fraction of scans]" min="0.0" max="1.0"
57 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." /> 57 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
58 <param name="min_run" type="float" value="12" label="Minimal elution time [unit corresponds to the retention time]" 58 <param name="min_run" type="float" value="12" label="Minimal elution time [unit corresponds to the retention time]"
59 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." /> 59 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
60 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]" 60 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]"
61 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value. 61 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value.
79 help="The lower limit of the ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function to fit the data." /> 79 help="The lower limit of the ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function to fit the data." />
80 <param name="sigma_ratio_lim_max" type="float" optional="true" label="Maximal sigma ratio" 80 <param name="sigma_ratio_lim_max" type="float" optional="true" label="Maximal sigma ratio"
81 help="The upper limit of the ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function to fit the data." /> 81 help="The upper limit of the ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function to fit the data." />
82 </section> 82 </section>
83 <conditional name="sd_cut"> 83 <conditional name="sd_cut">
84 <param name="sd_cut_bounds" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Standard deviations boundaries." 84 <param name="sd_cut_bounds" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Standard deviations boundaries."
85 help="Do not apply any limitations on the standard deviations." /> 85 help="Limit the standard deviations by setting boundaries." />
86 <when value="FALSE"> 86 <when value="TRUE">
87 <param name="sd_cut_min" type="float" value="0.01" label="Minimal standard deviation" 87 <param name="sd_cut_min" type="float" value="0.01" label="Minimal standard deviation"
88 help="The minimum standard deviation - features with a standard deviation lower than this number are eliminated." /> 88 help="The minimum standard deviation - features with a standard deviation lower than this number are eliminated." />
89 <param name="sd_cut_max" type="float" value="500" label="Maximal standard deviation" 89 <param name="sd_cut_max" type="float" value="500" label="Maximal standard deviation"
90 help="The maximum standard deviation - features with a standard deviation greater than this number are eliminated." /> 90 help="The maximum standard deviation - features with a standard deviation greater than this number are eliminated." />
91 </when> 91 </when>