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comparison xmsannotator_simple.xml @ 2:041052875af0 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit de75adf885d616bbe94c8087d3208a2b5039418e"
author recetox
date Thu, 08 Oct 2020 00:41:12 +0000
parents 97d1619ff23e
children 412d8bb4b54d
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1:02a38a19405d 2:041052875af0
1 <tool id="xmsannotator_simple" name="xMSannotator (simple)" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="xmsannotator_simple" name="xMSannotator (simple)" version="@TOOL_VERSION@+galaxy0">
2 <macros> 2 <macros>
3 <import>xmsannotator_macros.xml</import> 3 <import>xmsannotator_macros.xml</import>
4 </macros> 4 </macros>
5 5
6 <expand macro="requirements"/> 6 <requirements>
7 <container type="docker">@DOCKER_IMAGE@</container>
8 </requirements>
7 9
8 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
9 Rscript -e 'annotation <- xmsannotator::simple_annotation( 11 Rscript -e 'annotation <- xmsannotator::simple_annotation(
10 peaks = rhdf5::h5read("$peaks", "peaks"), 12 peaks = xmsannotator::load_hdf("$peaks", "peaks"),
11 adducts = rhdf5::h5read("$adducts", "adducts"), 13 adducts = xmsannotator::load_hdf("$adducts", "adducts"),
12 metabolites = rhdf5::h5read("$metabolites", "metabolites"), 14 compounds = xmsannotator::load_hdf("$compounds", "compounds"),
13 mz_tolerance_ppm = as.double($mz_tolerance_ppm) 15 mass_tolerance = 1e-6 * $mz_tolerance_ppm
14 )' 16 )'
15 -e 'rhdf5::h5write(annotation, "$annotation", "annotation")' 17 -e 'xmsannotator::save_hdf("$annotation", "annotation", annotation)'
16 ]]></command> 18 ]]></command>
17 19
18 <inputs> 20 <inputs>
19 <expand macro="annotation"/> 21 <expand macro="annotation"/>
20 </inputs> 22 </inputs>
23
21 <outputs> 24 <outputs>
22 <expand macro="output"/> 25 <data format="h5" name="annotation"/>
23 </outputs> 26 </outputs>
24 27
25 <help><![CDATA[ 28 <help><![CDATA[
26 Annotate the peak intensity table (such as outputted from apLCMS) with metabolites from the metabolite database. 29 Annotate the peak intensity table (such as outputted from apLCMS) with metabolites from the metabolite database.
27 30
28 The annotation process generates all possible metabolite-adduct pairs from the metabolite and adduct databases and matches those pairs to the measured peaks. 31 The annotation process generates all possible metabolite-adduct pairs from the metabolite and adduct databases and matches those pairs to the measured peaks.
29 A metabolite-adduct pair is pronounced as a match to the peak when the difference of their masses are withing some tolerance. 32 A metabolite-adduct pair is pronounced as a match to the peak when the difference of their masses are withing some tolerance.
30 ]]></help> 33 ]]></help>
34
31 <expand macro="citations"/> 35 <expand macro="citations"/>
32 </tool> 36 </tool>