Mercurial > repos > recetox > ramclustr_xcms

annotate 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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children 8f4d04ad4acd
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a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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1 <tool id="ramclustr_xcms" name="RAMClustR (XCMS)" version="@TOOL_VERSION@+galaxy0">
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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" />
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14 </inputs>
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15
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16 <command detect_errors="aggressive"><![CDATA[
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17 Rscript
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18 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
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19 -e 'x <- ramclustr_xcms(
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20 input_xcms = "$input_xcms",
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21 sr = $required.sr,
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22 deep_split = $required.deepSplit,
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23 block_size = $required.blocksize,
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24 mult = $required.mult,
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25 hmax = $required.hmax,
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26 collapse = $required.collapse,
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27 use_pheno = $required.usePheno,
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28 qc_inj_range = $required.qc_inj_range,
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29 normalize = "$required.normalize",
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30 min_module_size = $required.minModuleSize,
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31 linkage = "$required.linkage",
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32 mzdec = $required.mzdec,
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33 cor_method = "$required.cor_method",
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34 rt_only_low_n = $required.rt_only_low_n,
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35 replace_zeros = $required.replace_zeros,
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36 #if $optional.st
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37 st = $optional.st,
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38 #end if
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39 #if $optional.maxt
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40 maxt = $optional.maxt,
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41 #end if
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42 #if $optional.fftempdir
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43 fftempdir = $optional.fftempdir,
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44 #end if
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45 )'
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46 -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")'
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47 ]]>
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48 </command>
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49
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50 <outputs>
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51 <data label="${tool.name} on ${on_string}" name="result" format="RData" />
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52 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
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53 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
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54 <expand macro="output_msp"/>
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55 </outputs>
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56
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57 <tests>
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58 <test>
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59 <param name="input_xcms" value="xcmsObj.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
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60 <output name="result" file="ramclustObj.rdata" ftype="RData" compare="sim_size" delta="100"/>
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61 <output_collection name="mass_spectra" type="list">
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62 <element name="fill" file="fill.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/>
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63 </output_collection>
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64 <output name="method_metadata" file="metadata.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/>
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65 <output name="spec_abundance" file="spec_abundance.csv" ftype="csv" compare="sim_size" delta="100"/>
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66 </test>
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67 </tests>
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68
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69 <help>
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70 Documentation
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71 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
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72
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73 Upstream Tools
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74 +-------+----------------------+----------------------+------------+
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75 | Name | Output File | Format | Parameter |
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76 +=======+======================+======================+============+
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77 | xcms | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj |
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78 +-------+----------------------+----------------------+------------+
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79
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80 The tool takes an **xcmsSet** object as input and extracts all relevant information.
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81
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82 Downstream Tools
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83 +---------+--------------+----------------------+
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84 | Name | Output File | Format |
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85 +=========+==============+======================+
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86 | matchMS | Mass Spectra | collection (tgz/msp) |
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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87 +---------+--------------+----------------------+
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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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 @GENERAL_HELP@
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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90 </help>
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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91
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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92 <expand macro="citations" />
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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93 </tool>