Mercurial > repos > recetox > recetox_aplcms_generate_feature_table

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 0873c036d734782d2647b0eea84cd1a0658f5e58
author recetox
date Wed, 19 Jul 2023 00:25:16 +0000
parents fd078f5746d3
children
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1 <tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy2" profile="21.09">
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2 <description>generate feature table from noise-removed HRMS profile data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>help.xml</import>
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6 </macros>
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7 <edam_operations>
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8 <edam_operation>operation_3215</edam_operation>
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9 <edam_operation>operation_3799</edam_operation>
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10 </edam_operations>
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11 <expand macro="annotation"/>
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12 <expand macro="creator"/>
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13 <expand macro="requirements"/>
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15 <command detect_errors="aggressive"><![CDATA[
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16 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
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17 ]]></command>
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18 <configfiles>
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19 <configfile name="run_script"><![CDATA[
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20 profile <- load_data_from_parquet_file('$profile')
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21 sample_name <- load_sample_name(profile)
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23 if(is.na(sample_name)) {
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24 message("The file does not contain sample name.")
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25 }
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27 feature_table <- prof.to.features(
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28 profile = profile,
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29 bandwidth = $bandwidth,
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30 #if $min_bandwidth:
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31 min_bandwidth = $min_bandwidth,
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32 #else:
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33 min_bandwidth = NA,
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34 #end if
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35 #if $max_bandwidth:
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36 max_bandwidth = $max_bandwidth,
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37 #else:
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38 max_bandwidth = NA,
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39 #end if
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40 #if $advanced.sd_cut.sd_cut_bounds == "TRUE":
1
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41 sd_cut = c($advanced.sd_cut.sd_cut_min, $advanced.sd_cut.sd_cut_max),
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42 #else
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43 sd_cut = c(0, Inf),
0
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44 #end if
1
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45 sigma_ratio_lim = determine_sigma_ratios($advanced.shape_model.sigma_ratio_lim_min, $advanced.shape_model.sigma_ratio_lim_max),
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46 shape_model = "bi-Gaussian",
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47 peak_estim_method = "$advanced.peak_estim.peak_estim_method",
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48 component_eliminate = $advanced.component_eliminate,
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49 #if $advanced.peak_estim.peak_estim_method == "moment":
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50 moment_power = $advanced.peak_estim.moment_power,
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51 #else
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52 moment_power = 1,
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53 #end if
0
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54 BIC_factor = $BIC_factor,
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55 do.plot = FALSE
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56 )
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57
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58 feature_table <- save_sample_name(feature_table, sample_name)
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59 save_data_as_parquet_file(feature_table, '$output_file')
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60 ]]></configfile>
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61 </configfiles>
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62
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63 <inputs>
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64 <param label="Input profile data" name="profile" type="data" format="parquet"
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65 help="Mass spectrometry profile data." />
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66 <expand macro="bandwidth_params"/>
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67 <expand macro="generate_feature_table_params"/>
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68 </inputs>
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69
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70 <outputs>
3
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71 <data label="${($profile.element_identifier).rsplit('.',1)[0]}.parquet" name="output_file" format="parquet" />
0
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72 </outputs>
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73
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74 <tests>
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75
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76 </tests>
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78 <help>
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79 <![CDATA[
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80 @GENERATE_FEATURE_TABLE_HELP@
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81
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82 @GENERAL_HELP@
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83 ]]>
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84 </help>
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85
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86 <expand macro="citations"/>
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87 </tool>