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comparison macros.xml @ 0:b2253cf7db76 draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
author recetox
date Fri, 16 May 2025 08:02:01 +0000
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-1:000000000000 0:b2253cf7db76
1 <macros>
2 <token name="@TOOL_VERSION@">1.3.0</token>
3 <token name="@PROFILE@">23.0</token>
4
5 <xml name="citations">
6 <citations>
7 <citation type="doi">10.1021/acs.analchem.9b02354</citation>
8 <citation type="doi">10.1093/bioinformatics/btad455</citation>
9 </citations>
10 </xml>
11
12 <xml name="ionisation">
13 <param label="ionisation" name="ionisation" type="select" help="ionisation. positive +1 or negative -1">
14 <option value="1">positive</option>
15 <option value="-1">negative</option>
16 </param>
17 </xml>
18
19 <xml name="ppm">
20 <param name="ppm" type="float" value="100" min="0">
21 <label>ppm between isotopes</label>
22 <help>Maximum ppm value allowed between 2 isotopes. Default value 100.</help>
23 </param>
24 </xml>
25
26 <xml name="ms_unknown">
27 <param name="ppmunk" type="float" optional="true" min="0">
28 <label>ppm for unknown</label>
29 <help>ppm associated to the 'unknown' annotation. If not provided equal to ppm.</help>
30 </param>
31 <param name="ratiounk" type="float" optional="true" value="0.5" min="0">
32 <label>isotope ratio for unknown</label>
33 <help>isotope ratio associated to the 'unknown' annotation.</help>
34 </param>
35 </xml>
36
37 <xml name="ms_options">
38 <param name="ratiosd" type="float" value="0.9" optional="true" min="0">
39 <label>intensity ratio</label>
40 <help>acceptable ratio between predicted intensity and observed intensity of isotopes</help>
41 </param>
42 <param name="ppmthr" type="float" optional="true" min="0">
43 <label>ppm threshold</label>
44 <help>maximum ppm possible for the annotations. if not provided equal to 2*ppm.</help>
45 </param>
46 <param name="pRTNone" type="float" optional="true" value="0.8" min="0">
47 <label>no RT factor</label>
48 <help>multiplicative factor for the RT if no RTrange present in the database.</help>
49 </param>
50 <param name="pRTout" type="float" optional="true" value="0.4" min="0">
51 <label>outside RT factor</label>
52 <help>multiplicative factor for the RT if measured RT is outside the RTrange present in the database.</help>
53 </param>
54 </xml>
55 <xml name="gibbs">
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."/>
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."/>
58 <param label="gibbs sampler iterations" name="noits" type="integer" value="1000" help="number of iterations if the Gibbs sampler to be run."/>
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."/>
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."/>
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."/>
62 </xml>
63
64 <xml name="requirements">
65 <requirements>
66 <requirement type="package" version="@TOOL_VERSION@">ipapy2</requirement>
67 <requirement type="package" version="19.0.0">pyarrow</requirement>
68 <requirement type="package" version="2024.11.0">fastparquet</requirement>
69 </requirements>
70 </xml>
71 </macros>