Mercurial > repos > recetox > ramclustr_xcms

annotate ramclustr_wrapper.R @ 2:e46e0a0c13ca draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit beda1b99934fb8254de04bb38e41eb9ce836d71d"
author recetox
date Thu, 04 Feb 2021 11:34:30 +0000
parents 8f4d04ad4acd
children 405c8f8dc073
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a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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diff changeset
1 store_output <- function(
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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2 ramclustr_obj,
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3 output_filename,
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4 output_method_metadata,
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5 output_merge_msp,
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6 output_spec_abundance) {
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7 save(ramclustr_obj, file = output_filename)
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8 RAMClustR::write.methods(ramclustr_obj, output_method_metadata)
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9 RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp)
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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10 write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE)
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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11 }
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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12
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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13 ramclustr_xcms <- function(
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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14 input_xcms,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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15 sr,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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16 deep_split,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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17 block_size,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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18 mult,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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19 hmax,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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20 collapse,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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21 use_pheno,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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22 qc_inj_range,
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23 normalize,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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24 min_module_size,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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25 linkage,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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26 mzdec,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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27 cor_method,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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28 rt_only_low_n,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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29 replace_zeros,
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30 st = NULL,
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31 maxt = NULL,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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32 fftempdir = NULL
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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33 ) {
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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34 obj <- load(input_xcms)
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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35
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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36 x <- RAMClustR::ramclustR(
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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37 xcmsObj = xdata,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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38 st = st,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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39 maxt = maxt,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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40 sr = sr,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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41 deepSplit = deep_split,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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42 blocksize = block_size,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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43 mult = mult,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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44 hmax = hmax,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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45 collapse = collapse,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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46 usePheno = use_pheno,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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47 mspout = FALSE,
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48 qc.inj.range = qc_inj_range,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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49 normalize = normalize,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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50 minModuleSize = min_module_size,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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51 linkage = linkage,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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52 mzdec = mzdec,
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53 cor.method = cor_method,
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54 rt.only.low.n = rt_only_low_n,
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55 fftempdir = fftempdir,
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56 replace.zeros = replace_zeros
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57 )
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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58 return(x)
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59 }
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60
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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61 ramclustr_csv <- function(
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62 ms,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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63 idmsms,
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64 sample_name_column,
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65 feature_delimiter,
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66 retention_time_column,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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67 sr,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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68 deep_split,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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69 block_size,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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70 mult,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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71 hmax,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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72 collapse,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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73 use_pheno,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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74 qc_inj_range,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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75 normalize,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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76 min_module_size,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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77 linkage,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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78 mzdec,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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79 cor_method,
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80 rt_only_low_n,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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81 replace_zeros,
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82 st = NULL,
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83 maxt = NULL,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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84 fftempdir = NULL
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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85 ) {
1
8f4d04ad4acd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 36ea15ec5b1f1899f28c3a92d3a55dd6ac3dffae"
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86 if (!file.exists(idmsms))
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87 idmsms <- NULL
8f4d04ad4acd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 36ea15ec5b1f1899f28c3a92d3a55dd6ac3dffae"
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88
0
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89 x <- RAMClustR::ramclustR(
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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90 ms = ms,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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91 idmsms = idmsms,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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92 featdelim = feature_delimiter,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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93 timepos = retention_time_column,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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94 sampNameCol = sample_name_column,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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95 st = st,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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96 maxt = maxt,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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97 sr = sr,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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98 deepSplit = deep_split,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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99 blocksize = block_size,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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100 mult = mult,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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101 hmax = hmax,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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102 collapse = collapse,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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103 usePheno = use_pheno,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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104 mspout = FALSE,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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105 qc.inj.range = qc_inj_range,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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106 normalize = normalize,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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107 minModuleSize = min_module_size,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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108 linkage = linkage,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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109 mzdec = mzdec,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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110 cor.method = cor_method,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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111 rt.only.low.n = rt_only_low_n,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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112 fftempdir = fftempdir,
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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113 replace.zeros = replace_zeros
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114 )
a0c69d354b96 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
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115 return(x)
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116 }