Mercurial > repos > recetox > recetox_aplcms_generate_feature_table
comparison macros.xml @ 6:e7305ba0dd38 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 0873c036d734782d2647b0eea84cd1a0658f5e58
author | recetox |
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date | Wed, 19 Jul 2023 00:27:37 +0000 |
parents | 702a849c1e0e |
children | 32b66fb6a6a0 |
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5:702a849c1e0e | 6:e7305ba0dd38 |
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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> |