Mercurial > repos > recetox > recetox_aplcms_generate_feature_table

annotate recetox_aplcms_generate_feature_table.xml @ 1:e09137c38b4c draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
author recetox
date Mon, 03 Apr 2023 14:54:39 +0000
parents 17de8e7ce3ce
children b0423c52dce2
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1 <tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy0">
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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 <expand macro="creator"/>
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8 <expand macro="requirements"/>
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9
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10 <command detect_errors="aggressive"><![CDATA[
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11 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
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12 ]]></command>
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13 <configfiles>
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14 <configfile name="run_script"><![CDATA[
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15 profile <- load_data_from_parquet_file('$profile')
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16 sample_name <- load_sample_name(profile)
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17
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18 if(is.na(sample_name)) {
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19 message("The file does not contain sample name.")
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20 }
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22 feature_table <- prof.to.features(
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23 profile = profile,
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24 bandwidth = $bandwidth,
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25 #if $min_bandwidth:
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26 min_bandwidth = $min_bandwidth,
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27 #else:
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28 min_bandwidth = NA,
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29 #end if
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30 #if $max_bandwidth:
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31 max_bandwidth = $max_bandwidth,
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32 #else:
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33 max_bandwidth = NA,
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34 #end if
1
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35 #if $advanced.sd_cut.sd_cut_bounds == "FALSE":
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36 sd_cut = c($advanced.sd_cut.sd_cut_min, $advanced.sd_cut.sd_cut_max),
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37 #else
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38 sd_cut = c(0, Inf),
0
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39 #end if
1
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40 sigma_ratio_lim = determine_sigma_ratios($advanced.shape_model.sigma_ratio_lim_min, $advanced.shape_model.sigma_ratio_lim_max),
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41 shape_model = "bi-Gaussian",
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42 peak_estim_method = "$advanced.peak_estim.peak_estim_method",
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43 component_eliminate = $advanced.component_eliminate,
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44 #if $advanced.peak_estim.peak_estim_method == "moment":
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45 moment_power = $advanced.peak_estim.moment_power,
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46 #else
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47 moment_power = 1,
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48 #end if
0
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49 BIC_factor = $BIC_factor,
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50 do.plot = FALSE
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51 )
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52
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53 feature_table <- save_sample_name(feature_table, sample_name)
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54 save_data_as_parquet_file(feature_table, '$output_file')
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55 ]]></configfile>
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56 </configfiles>
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57
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58 <inputs>
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59 <param label="Input profile data" name="profile" type="data" format="parquet"
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60 help="Mass spectrometry profile data." />
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61 <expand macro="bandwidth_params"/>
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62 <expand macro="generate_feature_table_params"/>
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63 </inputs>
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64
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65 <outputs>
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66 <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" />
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67 </outputs>
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68
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69 <tests>
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70
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71 </tests>
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73 <help>
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74 <![CDATA[
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75 @GENERATE_FEATURE_TABLE_HELP@
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76
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77 @GENERAL_HELP@
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78 ]]>
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79 </help>
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80
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81 <expand macro="citations"/>
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82 </tool>