Mercurial > repos > recetox > recetox_aplcms_compute_clusters
comparison macros.xml @ 2:ce00e1d03c31 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
| author | recetox |
|---|---|
| date | Wed, 24 May 2023 14:48:47 +0000 |
| parents | 092bbb03a217 |
| children | 60a09c4fa7a0 |
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| 1:092bbb03a217 | 2:ce00e1d03c31 |
|---|---|
| 1 <macros> | 1 <macros> |
| 2 <token name="@TOOL_VERSION@">0.10.3</token> | 2 <token name="@TOOL_VERSION@">0.11.0</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> |
| 91 </when> | 91 </when> |
| 92 </conditional> | 92 </conditional> |
| 93 </section> | 93 </section> |
| 94 </xml> | 94 </xml> |
| 95 | 95 |
| 96 <xml name="compute_clusters_params"> | 96 <xml name="tolerances"> |
| 97 <conditional name="tolerances_input_method"> | 97 <param name="mz_tol_relative_ppm" type="float" value="10" label="Relative m/z tolerance [ppm]" |
| 98 <param name="input_method" type="select" display="radio" label="Tolerances input method" | 98 help="Relative m/z tolerance to use for grouping features." /> |
| 99 help="Tolerances can be entered directly or loaded from a file."> | 99 <param name="rt_tol" type="float" value="5" label="Retention time tolerance [unit corresponds to the retention time]" |
| 100 <option value="direct" selected="true">direct</option> | 100 help="Retention time tolerance to use for grouping features." /> |
| 101 <option value="file">file</option> | |
| 102 </param> | |
| 103 <when value="direct"> | |
| 104 <param name="mz_tol_relative" type="float" optional="true" label="Relative m/z tolerance" | |
| 105 help="Relative m/z tolerance to use for grouping features. | |
| 106 If not provided, it is calculated from the data using kernel density estimation." /> | |
| 107 <param name="rt_tol_relative" type="float" optional="true" label="Relative rt tolerance [unit corresponds to the retention time]" | |
| 108 help="Relative retention time tolerance to use for grouping features. | |
| 109 If not provided, it is calculated from the data using kernel density estimation." /> | |
| 110 </when> | |
| 111 <when value="file"> | |
| 112 <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet" | |
| 113 help="Table containing tolerance values." /> | |
| 114 </when> | |
| 115 </conditional> | |
| 116 <param name="mz_tol_absolute" type="float" label="Minimal absolute m/z tolerance [Da]" value="1e-05" | |
| 117 help="During the clustering, an m/z tolerance is computed based on the data and the specified relative tolerance. | |
| 118 This parameter allows the specification of a minimal value of this tolerance." /> | |
| 119 <param name="mz_max_diff" type="float" label="Maximal m/z difference [Da]" value="0.01" | |
| 120 help="Maximum allowed difference between feature m/z values to belong to the same cluster." /> | |
| 121 | |
| 122 </xml> | 101 </xml> |
| 123 | 102 |
| 124 <xml name="recover_weaker_params"> | 103 <xml name="recover_weaker_params"> |
| 125 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]" | 104 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]" |
| 126 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value. | 105 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value. |