Mercurial > repos > recetox > ramclustr_csv

annotate ramclustr_csv.xml @ 0:43b60b28ccf7 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 22:14:48 +0000
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children d9c9ec0e2bd8
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1 <tool id="ramclustr_csv" name="RAMClustR (CSV)" 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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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 <expand macro="parameters_csv" />
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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("${__tool_directory__}/ramclustr_wrapper.R")'
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19 -e 'x <- ramclustr_csv(
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20 ms="$ms_csv.ms",
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21 idmsms="$ms_csv.idmsms",
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22 feature_delimiter="$ms_csv.feature_delimiter",
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23 sample_name_column = $ms_csv.sample_name_column,
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24 retention_time_column= $ms_csv.retention_time_column,
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25 sr = $required.sr,
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26 deep_split = $required.deepSplit,
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27 block_size = $required.blocksize,
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28 mult = $required.mult,
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29 hmax = $required.hmax,
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30 collapse = $required.collapse,
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31 use_pheno = $required.usePheno,
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32 qc_inj_range = $required.qc_inj_range,
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33 normalize = "$required.normalize",
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34 min_module_size = $required.minModuleSize,
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35 linkage = "$required.linkage",
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36 mzdec = $required.mzdec,
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37 cor_method = "$required.cor_method",
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38 rt_only_low_n = $required.rt_only_low_n,
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39 replace_zeros = $required.replace_zeros,
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40 #if $optional.st
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41 st = $optional.st,
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42 #end if
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43 #if $optional.maxt
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44 maxt = $optional.maxt,
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45 #end if
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46 #if $optional.fftempdir
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47 fftempdir = $optional.fftempdir,
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48 #end if
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49 )'
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50 -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")'
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51
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52 ]]>
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53 </command>
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54
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55 <outputs>
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56 <data label="${tool.name} on ${on_string}" name="result" format="RData" />
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57 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
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58 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
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59 <expand macro="output_msp"/>
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60 </outputs>
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61
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62 <help>
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63 Documentation
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64 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
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65
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66 Upstream Tools
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67 +-------+------------------------+--------+------------+
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68 | Name | Output File | Format | Parameter |
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69 +=======+========================+========+============+
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70 | ??? | Feature Table with MS1 | csv | ms |
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71 +-------+------------------------+--------+------------+
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72 | ??? | Feature Table with MS2 | csv | idmsms |
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73 +-------+------------------------+--------+------------+
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74
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75 The tool takes a **csv** table as input which has to fulfill the following requirements
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76
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77 (1) no more than one sample (or file) name column and one feature name row;
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78 (2) feature names that contain the mass and retention times, separated by a constant delimiter; and
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79 (3) features in columns and samples in rows.
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80
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81 Downstream Tools
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82 +---------+--------------+----------------------+
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83 | Name | Output File | Format |
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84 +=========+==============+======================+
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85 | matchMS | Mass Spectra | collection (tgz/msp) |
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86 +---------+--------------+----------------------+
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87
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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88 @GENERAL_HELP@
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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89 </help>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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90
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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91 <expand macro="citations" />
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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92 </tool>