Mercurial > repos > recetox > ramclustr_xcms

annotate 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
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1 <tool id="ramclustr_xcms" name="RAMClustR (XCMS)" version="@TOOL_VERSION@+galaxy1">
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2 <macros>
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3 <import>ramclustr_macros.xml</import>
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4 </macros>
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5
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6 <requirements>
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7 <container type="docker">recetox/ramclustr:1.1.0-recetox0</container>
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8 </requirements>
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9
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10 <inputs>
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11 <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help=": containing grouped feature data for clustering by ramclustR" />
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12 <expand macro="parameters_required" />
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13 <expand macro="parameters_optional_xcms" />
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14 <expand macro="parameters_optional_metadata" />
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15 </inputs>
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17 <command detect_errors="aggressive"><![CDATA[
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18 Rscript
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19 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
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20 -e 'x <- ramclustr_xcms(
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21 input_xcms = "$input_xcms",
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22 sr = $required.sr,
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23 deep_split = $required.deepSplit,
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24 block_size = $required.blocksize,
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25 mult = $required.mult,
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26 hmax = $required.hmax,
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27 collapse = $required.collapse,
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28 use_pheno = $required.usePheno,
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29 qc_inj_range = $required.qc_inj_range,
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30 normalize = "$required.normalize",
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31 min_module_size = $required.minModuleSize,
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32 linkage = "$required.linkage",
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33 mzdec = $required.mzdec,
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34 cor_method = "$required.cor_method",
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35 rt_only_low_n = $required.rt_only_low_n,
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36 replace_zeros = $required.replace_zeros,
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37 #if $optional.st
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38 st = $optional.st,
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39 #end if
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40 #if $optional.maxt
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41 maxt = $optional.maxt,
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42 #end if
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43 #if $optional.fftempdir
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44 fftempdir = $optional.fftempdir,
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45 #end if
3
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46 #if $metadata.batch_order_qc
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47 metadata_file = "${metadata.batch_order_qc}",
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48 #end if
0
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49 )'
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50 -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")'
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51 ]]>
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52 </command>
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53
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54 <outputs>
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55 <data label="${tool.name} on ${on_string}" name="result" format="RData" />
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56 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
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57 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
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58 <expand macro="output_msp"/>
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59 </outputs>
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60
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61 <tests>
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62 <test>
3
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63 <param name="input_xcms" value="xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
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64 <output name="result" file="ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="100"/>
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65 <output_collection name="mass_spectra" type="list">
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66 <element name="fill" file="fill_xcms_1.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/>
0
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67 </output_collection>
3
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68 <output name="method_metadata" file="metadata_xcms_1.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/>
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69 <output name="spec_abundance" file="spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
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70 </test>
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71 <test>
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72 <param name="input_xcms" value="xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
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73 <param name="batch_order_qc" value="sample_metadata_xcms_2.csv" ftype="csv" />
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74 <output name="result" file="ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
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75 <output_collection name="mass_spectra" type="list">
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76 <element name="fill" file="fill_xcms_2.msp" ftype="msp" lines_diff="10"/>
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77 </output_collection>
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78 <output name="method_metadata" file="metadata_xcms_2.txt" ftype="txt" checksum="md5$286e4aa53c38c99e92202584d7407406"/>
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79 <output name="spec_abundance" file="spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
0
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80 </test>
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81 </tests>
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82
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83 <help>
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84 Documentation
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85 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
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86
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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87 Upstream Tools
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88 +-------+----------------------+----------------------+------------+
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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89 | Name | Output File | Format | Parameter |
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90 +=======+======================+======================+============+
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91 | xcms | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj |
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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92 +-------+----------------------+----------------------+------------+
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93
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94 The tool takes an **xcmsSet** object as input and extracts all relevant information.
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95
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96 Downstream Tools
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97 +---------+--------------+----------------------+
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98 | Name | Output File | Format |
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99 +=========+==============+======================+
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100 | matchMS | Mass Spectra | collection (tgz/msp) |
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101 +---------+--------------+----------------------+
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102
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103 @GENERAL_HELP@
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104 </help>
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105
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106 <expand macro="citations" />
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107 </tool>