annotate macros.xml @ 0:cb18b8fcb441 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
author recetox
date Fri, 16 May 2025 08:02:15 +0000
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cb18b8fcb441 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.3.0</token>
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3 <token name="@PROFILE@">23.0</token>
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4
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5 <xml name="citations">
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6 <citations>
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7 <citation type="doi">10.1021/acs.analchem.9b02354</citation>
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8 <citation type="doi">10.1093/bioinformatics/btad455</citation>
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9 </citations>
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10 </xml>
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11
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12 <xml name="ionisation">
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13 <param label="ionisation" name="ionisation" type="select" help="ionisation. positive +1 or negative -1">
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14 <option value="1">positive</option>
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15 <option value="-1">negative</option>
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16 </param>
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17 </xml>
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18
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19 <xml name="ppm">
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20 <param name="ppm" type="float" value="100" min="0">
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21 <label>ppm between isotopes</label>
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22 <help>Maximum ppm value allowed between 2 isotopes. Default value 100.</help>
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23 </param>
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24 </xml>
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25
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26 <xml name="ms_unknown">
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27 <param name="ppmunk" type="float" optional="true" min="0">
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28 <label>ppm for unknown</label>
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29 <help>ppm associated to the 'unknown' annotation. If not provided equal to ppm.</help>
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30 </param>
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31 <param name="ratiounk" type="float" optional="true" value="0.5" min="0">
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32 <label>isotope ratio for unknown</label>
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33 <help>isotope ratio associated to the 'unknown' annotation.</help>
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34 </param>
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35 </xml>
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36
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37 <xml name="ms_options">
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38 <param name="ratiosd" type="float" value="0.9" optional="true" min="0">
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39 <label>intensity ratio</label>
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40 <help>acceptable ratio between predicted intensity and observed intensity of isotopes</help>
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41 </param>
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42 <param name="ppmthr" type="float" optional="true" min="0">
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43 <label>ppm threshold</label>
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44 <help>maximum ppm possible for the annotations. if not provided equal to 2*ppm.</help>
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45 </param>
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46 <param name="pRTNone" type="float" optional="true" value="0.8" min="0">
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47 <label>no RT factor</label>
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48 <help>multiplicative factor for the RT if no RTrange present in the database.</help>
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49 </param>
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50 <param name="pRTout" type="float" optional="true" value="0.4" min="0">
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51 <label>outside RT factor</label>
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52 <help>multiplicative factor for the RT if measured RT is outside the RTrange present in the database.</help>
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53 </param>
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54 </xml>
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55 <xml name="gibbs">
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56 <param label="Mapped isotope patterns" name="mapped_isotope_patterns" type="data" format="csv,tsv,tabular,parquet" help="A csv file containing the MS1 data. Ideally obtained from map_isotope_patterns."/>
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57 <param label="annotations" name="annotations" type="data" format="csv,tsv,tabular,parquet" help="pandas dataframe containing all the possible annotations for the measured features."/>
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58 <param label="gibbs sampler iterations" name="noits" type="integer" value="1000" help="number of iterations if the Gibbs sampler to be run."/>
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59 <param label="ignored iterations" name="burn" type="integer" optional="true" value="10" help="number of iterations to be ignored when computing posterior probabilities. If None, is set to 10% of total iterations."/>
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60 <param label="output Gibbs parameter" name="all_out" type="boolean" value="false" optional="true" help="logical value. If true the list of assignments found in each iteration is returned by the function. Default False."/>
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61 <param label="previous Gibbs sampler" name="zs" type="data" format="txt" optional="true" help="list of assignments computed in a previous run of the Gibbs sampler. Optional, default None."/>
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62 </xml>
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63
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64 <xml name="requirements">
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65 <requirements>
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66 <requirement type="package" version="@TOOL_VERSION@">ipapy2</requirement>
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67 <requirement type="package" version="19.0.0">pyarrow</requirement>
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68 <requirement type="package" version="2024.11.0">fastparquet</requirement>
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69 </requirements>
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70 </xml>
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71 </macros>