Mercurial > repos > recetox > recetox_aplcms_align_features

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author recetox
date Wed, 03 May 2023 15:18:57 +0000
parents 1e2a13bcb5a7
children c44c73efd6e5
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1 <tool id="recetox_aplcms_align_features" name="recetox-aplcms - align features" version="@TOOL_VERSION@+galaxy0">
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2 <description>align peaks across samples</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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10 <command detect_errors="aggressive"><![CDATA[
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11 Rscript -e "cluster <- \${GALAXY_SLOTS:-1}" -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 #set filenames = str("', '").join([str($f) for $f in $files])
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16 feature_tables <- load_parquet_collection(c('$filenames'))
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17 sample_names <- unlist(lapply(feature_tables, load_sample_name))
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19 validate_sample_names(sample_names)
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21 ordering <- order(sample_names)
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22 feature_tables <- feature_tables[ordering]
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23 sample_names <- sample_names[ordering]
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25 tolerances <- load_data_from_parquet_file('$input_tolerances')
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27 aligned_features <- create_aligned_feature_table(
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28 features_table = dplyr::bind_rows(feature_tables),
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29 min_occurrence = $min_occurrence,
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30 sample_names = sample_names,
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31 mz_tol_relative = get_mz_tol(tolerances),
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32 rt_tol_relative = get_rt_tol(tolerances),
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33 cluster = cluster
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34 )
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36 save_aligned_features(aligned_features, '$metadata_file', '$rt_file', '$intensity_file')
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37 ]]></configfile>
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38 </configfiles>
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40 <inputs>
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41 <param name="files" type="data_collection" collection_type="list" format="parquet"
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42 label="Clustered features" help="List of tables containing clustered features." />
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43 <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet"
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44 help="Table containing tolerance values." />
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45 <param name="min_occurrence" type="integer" min="2" value="2" label="Minimal occurrence in samples"
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46 help="A feature has to show up in at least this number of profiles to be included in the final result." />
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47 </inputs>
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49 <outputs>
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50 <data name="metadata_file" format="parquet" label="${tool.name} on ${on_string} (metadata table)"/>
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51 <data name="rt_file" format="parquet" label="${tool.name} on ${on_string} (rt table)"/>
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52 <data name="intensity_file" format="parquet" label="${tool.name} on ${on_string} (intensity table)"/>
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53 </outputs>
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55 <tests>
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56
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57 </tests>
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59 <help>
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60 <![CDATA[
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61 @ALIGN_FEATURES_HELP@
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63 @GENERAL_HELP@
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64 ]]>
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65 </help>
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67 <expand macro="citations"/>
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68 </tool>