Mercurial > repos > recetox > ramclustr_xcms

comparison ramclustr_xcms.xml @ 3:405c8f8dc073 draft default tip

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
author recetox
date Mon, 07 Jun 2021 15:12:58 +0000
parents 8f4d04ad4acd
children
comparison
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2:e46e0a0c13ca 3:405c8f8dc073
1 <tool id="ramclustr_xcms" name="RAMClustR (XCMS)" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="ramclustr_xcms" name="RAMClustR (XCMS)" version="@TOOL_VERSION@+galaxy1">
2 <macros> 2 <macros>
3 <import>ramclustr_macros.xml</import> 3 <import>ramclustr_macros.xml</import>
4 </macros> 4 </macros>
5 5
6 <requirements> 6 <requirements>
9 9
10 <inputs> 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" /> 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" /> 12 <expand macro="parameters_required" />
13 <expand macro="parameters_optional_xcms" /> 13 <expand macro="parameters_optional_xcms" />
14 <expand macro="parameters_optional_metadata" />
14 </inputs> 15 </inputs>
15 16
16 <command detect_errors="aggressive"><![CDATA[ 17 <command detect_errors="aggressive"><![CDATA[
17 Rscript 18 Rscript
18 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")' 19 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
40 maxt = $optional.maxt, 41 maxt = $optional.maxt,
41 #end if 42 #end if
42 #if $optional.fftempdir 43 #if $optional.fftempdir
43 fftempdir = $optional.fftempdir, 44 fftempdir = $optional.fftempdir,
44 #end if 45 #end if
46 #if $metadata.batch_order_qc
47 metadata_file = "${metadata.batch_order_qc}",
48 #end if
45 )' 49 )'
46 -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")' 50 -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")'
47 ]]> 51 ]]>
48 </command> 52 </command>
49 53
54 <expand macro="output_msp"/> 58 <expand macro="output_msp"/>
55 </outputs> 59 </outputs>
56 60
57 <tests> 61 <tests>
58 <test> 62 <test>
59 <param name="input_xcms" value="xcmsObj.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/> 63 <param name="input_xcms" value="xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
60 <output name="result" file="ramclustObj.rdata" ftype="RData" compare="sim_size" delta="100"/> 64 <output name="result" file="ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="100"/>
61 <output_collection name="mass_spectra" type="list"> 65 <output_collection name="mass_spectra" type="list">
62 <element name="fill" file="fill.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/> 66 <element name="fill" file="fill_xcms_1.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/>
63 </output_collection> 67 </output_collection>
64 <output name="method_metadata" file="metadata.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/> 68 <output name="method_metadata" file="metadata_xcms_1.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/>
65 <output name="spec_abundance" file="spec_abundance.csv" ftype="csv" compare="sim_size" delta="100"/> 69 <output name="spec_abundance" file="spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
70 </test>
71 <test>
72 <param name="input_xcms" value="xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
73 <param name="batch_order_qc" value="sample_metadata_xcms_2.csv" ftype="csv" />
74 <output name="result" file="ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
75 <output_collection name="mass_spectra" type="list">
76 <element name="fill" file="fill_xcms_2.msp" ftype="msp" lines_diff="10"/>
77 </output_collection>
78 <output name="method_metadata" file="metadata_xcms_2.txt" ftype="txt" checksum="md5$286e4aa53c38c99e92202584d7407406"/>
79 <output name="spec_abundance" file="spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
66 </test> 80 </test>
67 </tests> 81 </tests>
68 82
69 <help> 83 <help>
70 Documentation 84 Documentation