Mercurial > repos > recetox > xmsannotator_simple

annotate xmsannotator_macros.xml @ 5:9540eaefa2f1 draft default tip

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/xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
author recetox
date Thu, 12 Aug 2021 11:13:26 +0000
parents cd0729b7c3dc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
1 <macros>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
2 <token name="@TOOL_VERSION@">1.3.2</token>
4
cd0729b7c3dc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit b99706e26938905c4d75763e3041f69fba4bff71"
recetox
parents: 3
diff changeset
3 <token name="@DOCKER_IMAGE@">recetox/xmsannotator:1.3.2-recetox3</token>
0
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
4
5
9540eaefa2f1 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
recetox
parents: 4
diff changeset
5 <xml name="creator">
9540eaefa2f1 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
recetox
parents: 4
diff changeset
6 <creator>
9540eaefa2f1 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
recetox
parents: 4
diff changeset
7 <organization
9540eaefa2f1 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
recetox
parents: 4
diff changeset
8 url="https://www.recetox.muni.cz/"
9540eaefa2f1 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
recetox
parents: 4
diff changeset
9 name="RECETOX MUNI" />
9540eaefa2f1 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
recetox
parents: 4
diff changeset
10 </creator>
9540eaefa2f1 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
recetox
parents: 4
diff changeset
11 </xml>
9540eaefa2f1 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
recetox
parents: 4
diff changeset
12
3
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
13 <xml name="inputs">
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
14 <param name="peak_table" type="data" format="csv,h5,parquet">
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
15 <label>Peak table</label>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
16 <help><![CDATA[
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
17 A peak-intensity table such as outputted from apLCMS.
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
18 The file is required to contain the fields <em>mz</em> and <em>rt</em>.
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
19 ]]></help>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
20 </param>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
21 <param name="compound_table" type="data" format="csv,parquet">
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
22 <label>Compound database</label>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
23 <help><![CDATA[
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
24 Database of compounds according to which the annotation is performed.
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
25 The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
26 ]]></help>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
27 </param>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
28 <param name="adduct_table" type="data" format="csv,parquet" optional="true">
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
29 <label>Adduct database (optional)</label>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
30 <help><![CDATA[
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
31 Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
32 The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
33 ]]></help>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
34 </param>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
35 </xml>
0
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
36
3
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
37 <xml name="outputs">
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
38 <data name="annotation_parquet" format="parquet"/>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
39 </xml>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
40
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
41 <xml name="tolerance">
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
42 <param name="mass_tolerance_ppm" type="integer" min="0" value="5">
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
43 <label>Mass tolerance [ppm]</label>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
44 <help>Mass tolerance in ppm for database matching.</help>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
45 </param>
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
46 <yield/>
0
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
47 </xml>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
48
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
49 <xml name="citations">
3
412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
recetox
parents: 2
diff changeset
50 <citation type="doi">10.1021/acs.analchem.6b01214</citation>
0
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
51 </xml>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
52 </macros>