Mercurial > repos > recetox > ramclustr_xcms

comparison ramclustr_xcms.xml @ 0:a0c69d354b96 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
author recetox
date Mon, 07 Dec 2020 22:14:20 +0000
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-1:000000000000 0:a0c69d354b96
1 <tool id="ramclustr_xcms" name="RAMClustR (XCMS)" version="@TOOL_VERSION@+galaxy0">
2 <macros>
3 <import>ramclustr_macros.xml</import>
4 </macros>
5
6 <requirements>
7 <container type="docker">recetox/ramclustr:1.1.0-recetox0</container>
8 </requirements>
9
10 <inputs>
11 <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help=": containing grouped feature data for clustering by ramclustR" />
12 <expand macro="parameters_required" />
13 <expand macro="parameters_optional" />
14 </inputs>
15
16 <command detect_errors="aggressive"><![CDATA[
17 Rscript
18 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
19 -e 'x <- ramclustr_xcms(
20 input_xcms = "$input_xcms",
21 sr = $required.sr,
22 deep_split = $required.deepSplit,
23 block_size = $required.blocksize,
24 mult = $required.mult,
25 hmax = $required.hmax,
26 collapse = $required.collapse,
27 use_pheno = $required.usePheno,
28 qc_inj_range = $required.qc_inj_range,
29 normalize = "$required.normalize",
30 min_module_size = $required.minModuleSize,
31 linkage = "$required.linkage",
32 mzdec = $required.mzdec,
33 cor_method = "$required.cor_method",
34 rt_only_low_n = $required.rt_only_low_n,
35 replace_zeros = $required.replace_zeros,
36 #if $optional.st
37 st = $optional.st,
38 #end if
39 #if $optional.maxt
40 maxt = $optional.maxt,
41 #end if
42 #if $optional.fftempdir
43 fftempdir = $optional.fftempdir,
44 #end if
45 )'
46 -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")'
47 ]]>
48 </command>
49
50 <outputs>
51 <data label="${tool.name} on ${on_string}" name="result" format="RData" />
52 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
53 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
54 <expand macro="output_msp"/>
55 </outputs>
56
57 <tests>
58 <test>
59 <param name="input_xcms" value="xcmsObj.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
60 <output name="result" file="ramclustObj.rdata" ftype="RData" compare="sim_size" delta="100"/>
61 <output_collection name="mass_spectra" type="list">
62 <element name="fill" file="fill.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/>
63 </output_collection>
64 <output name="method_metadata" file="metadata.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/>
65 <output name="spec_abundance" file="spec_abundance.csv" ftype="csv" compare="sim_size" delta="100"/>
66 </test>
67 </tests>
68
69 <help>
70 Documentation
71 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
72
73 Upstream Tools
74 +-------+----------------------+----------------------+------------+
75 | Name | Output File | Format | Parameter |
76 +=======+======================+======================+============+
77 | xcms | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj |
78 +-------+----------------------+----------------------+------------+
79
80 The tool takes an **xcmsSet** object as input and extracts all relevant information.
81
82 Downstream Tools
83 +---------+--------------+----------------------+
84 | Name | Output File | Format |
85 +=========+==============+======================+
86 | matchMS | Mass Spectra | collection (tgz/msp) |
87 +---------+--------------+----------------------+
88
89 @GENERAL_HELP@
90 </help>
91
92 <expand macro="citations" />
93 </tool>