Mercurial > repos > recetox > recetox_aplcms_remove_noise
comparison macros.xml @ 6:d90187b0f247 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 0873c036d734782d2647b0eea84cd1a0658f5e58
| author | recetox |
|---|---|
| date | Wed, 19 Jul 2023 00:26:32 +0000 |
| parents | 156293ea9f88 |
| children | 12bf74dd09f1 |
comparison
equal
deleted
inserted
replaced
| 5:156293ea9f88 | 6:d90187b0f247 |
|---|---|
| 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> |