Mercurial > repos > recetox > ipapy2_clustering
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 |
parents | |
children |
rev | line source |
---|---|
0
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
1 <macros> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
2 <token name="@TOOL_VERSION@">1.3.0</token> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
3 <token name="@PROFILE@">23.0</token> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
4 |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
5 <xml name="citations"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
6 <citations> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
7 <citation type="doi">10.1021/acs.analchem.9b02354</citation> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
8 <citation type="doi">10.1093/bioinformatics/btad455</citation> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
9 </citations> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
10 </xml> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
11 |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
12 <xml name="ionisation"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
13 <param label="ionisation" name="ionisation" type="select" help="ionisation. positive +1 or negative -1"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
14 <option value="1">positive</option> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
15 <option value="-1">negative</option> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
16 </param> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
17 </xml> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
18 |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
19 <xml name="ppm"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
20 <param name="ppm" type="float" value="100" min="0"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
21 <label>ppm between isotopes</label> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
22 <help>Maximum ppm value allowed between 2 isotopes. Default value 100.</help> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
23 </param> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
24 </xml> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
25 |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
26 <xml name="ms_unknown"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
27 <param name="ppmunk" type="float" optional="true" min="0"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
28 <label>ppm for unknown</label> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
29 <help>ppm associated to the 'unknown' annotation. If not provided equal to ppm.</help> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
30 </param> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
31 <param name="ratiounk" type="float" optional="true" value="0.5" min="0"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
32 <label>isotope ratio for unknown</label> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
33 <help>isotope ratio associated to the 'unknown' annotation.</help> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
34 </param> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
35 </xml> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
36 |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
37 <xml name="ms_options"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
38 <param name="ratiosd" type="float" value="0.9" optional="true" min="0"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
39 <label>intensity ratio</label> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
40 <help>acceptable ratio between predicted intensity and observed intensity of isotopes</help> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
41 </param> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
42 <param name="ppmthr" type="float" optional="true" min="0"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
43 <label>ppm threshold</label> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
44 <help>maximum ppm possible for the annotations. if not provided equal to 2*ppm.</help> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
45 </param> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
46 <param name="pRTNone" type="float" optional="true" value="0.8" min="0"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
47 <label>no RT factor</label> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
48 <help>multiplicative factor for the RT if no RTrange present in the database.</help> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
49 </param> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
50 <param name="pRTout" type="float" optional="true" value="0.4" min="0"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
51 <label>outside RT factor</label> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
52 <help>multiplicative factor for the RT if measured RT is outside the RTrange present in the database.</help> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
53 </param> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
54 </xml> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
55 <xml name="gibbs"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
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."/> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
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."/> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
58 <param label="gibbs sampler iterations" name="noits" type="integer" value="1000" help="number of iterations if the Gibbs sampler to be run."/> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
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."/> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
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."/> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
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."/> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
62 </xml> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
63 |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
64 <xml name="requirements"> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
65 <requirements> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
66 <requirement type="package" version="@TOOL_VERSION@">ipapy2</requirement> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
67 <requirement type="package" version="19.0.0">pyarrow</requirement> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
68 <requirement type="package" version="2024.11.0">fastparquet</requirement> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
69 </requirements> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
70 </xml> |
cb18b8fcb441
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
recetox
parents:
diff
changeset
|
71 </macros> |