Mercurial > repos > recetox > october_recetox_xmsannotator_advanced

annotate macros.xml @ 2:116ec7c1c038 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c5af7c9cf5389414b71b6324e7241433c35c9bb0"
author recetox
date Fri, 29 Oct 2021 13:15:04 +0000
parents 8fcf5ca25f5d
children 10a389dc2cc7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
1 <macros>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
2 <token name="@TOOL_VERSION@">0.9.0</token>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
3 <xml name="requirements">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
4 <requirements>
2
116ec7c1c038 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c5af7c9cf5389414b71b6324e7241433c35c9bb0"
recetox
parents: 1
diff changeset
5 <container type="docker">recetox/recetox-xmsannotator:october5</container>
0
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
6 </requirements>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
7 </xml>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
8 <xml name="creator">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
9 <creator>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
10 <organization
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
11 url="https://www.recetox.muni.cz/"
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
12 name="RECETOX MUNI" />
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
13 </creator>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
14 </xml>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
15 <xml name="inputs">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
16 <param name="peak_table" type="data" format="csv,parquet">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
17 <label>Peak table</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
18 <help><![CDATA[
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
19 A peak-intensity table such as outputted from apLCMS.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
20 The file is required to contain the fields <em>mz</em> and <em>rt</em>.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
21 Columns for feature intensity in a sample have to start with <em>intensity</em>.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
22
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
23 ]]></help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
24 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
25 <param name="compound_table" type="data" format="csv,parquet">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
26 <label>Compound database</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
27 <help><![CDATA[
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
28 Database of compounds according to which the annotation is performed.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
29 The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
30 ]]></help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
31 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
32 <param name="adduct_table" type="data" format="csv,parquet" optional="true">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
33 <label>Adduct database (optional)</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
34 <help><![CDATA[
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
35 Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
36 The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
37 ]]></help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
38 </param>
1
8fcf5ca25f5d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit b26a7ce6459f8e456fd166ba1aaada4e7e66dfa6"
recetox
parents: 0
diff changeset
39 <param name="adduct_weights" type="data" format="csv" optional="true">
8fcf5ca25f5d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit b26a7ce6459f8e456fd166ba1aaada4e7e66dfa6"
recetox
parents: 0
diff changeset
40 <label>adduct_weights</label>
8fcf5ca25f5d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit b26a7ce6459f8e456fd166ba1aaada4e7e66dfa6"
recetox
parents: 0
diff changeset
41 </param>
0
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
42 </xml>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
43
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
44 <xml name="outputs">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
45 <data name="annotation_parquet" format="parquet"/>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
46 </xml>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
47
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
48 <xml name="tolerance">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
49 <param name="mass_tolerance_ppm" type="integer" min="0" value="5">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
50 <label>Mass tolerance [ppm]</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
51 <help>Mass tolerance in ppm for database matching.</help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
52 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
53 <yield/>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
54 </xml>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
55 <token name="@HELP@">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
56 <![CDATA[
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
57 Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
58 using advanced methods.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
59
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
60 The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
61 peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
62 withing some tolerance.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
63 ]]>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
64 </token>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
65 <xml name="citations">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
66 <citation type="doi">10.1021/acs.analchem.6b01214</citation>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
67 </xml>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
68 </macros>