Mercurial > repos > recetox > xmsannotator_simple

annotate xmsannotator_simple.xml @ 0:97d1619ff23e 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/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
author recetox
date Wed, 23 Sep 2020 13:31:39 +0000
parents
children 041052875af0
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 <tool id="xmsannotator_simple" name="xMSannotator (simple)" version="@TOOL_VERSION@+galaxy0">
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
2 <macros>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
3 <import>xmsannotator_macros.xml</import>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
4 </macros>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
5
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
6 <expand macro="requirements"/>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
7
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
8 <command detect_errors="aggressive"><![CDATA[
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
9 Rscript -e 'annotation <- xmsannotator::simple_annotation(
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
10 peaks = rhdf5::h5read("$peaks", "peaks"),
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
11 adducts = rhdf5::h5read("$adducts", "adducts"),
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
12 metabolites = rhdf5::h5read("$metabolites", "metabolites"),
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
13 mz_tolerance_ppm = as.double($mz_tolerance_ppm)
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
14 )'
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
15 -e 'rhdf5::h5write(annotation, "$annotation", "annotation")'
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
16 ]]></command>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
17
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
18 <inputs>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
19 <expand macro="annotation"/>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
20 </inputs>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
21 <outputs>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
22 <expand macro="output"/>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
23 </outputs>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
24
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
25 <help><![CDATA[
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
26 Annotate the peak intensity table (such as outputted from apLCMS) with metabolites from the metabolite database.
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
27
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
28 The annotation process generates all possible metabolite-adduct pairs from the metabolite and adduct databases and matches those pairs to the measured peaks.
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
29 A metabolite-adduct pair is pronounced as a match to the peak when the difference of their masses are withing some tolerance.
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
30 ]]></help>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
31 <expand macro="citations"/>
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
recetox
parents:
diff changeset
32 </tool>