Mercurial > repos > recetox > recetox_aplcms_compute_clusters

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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 00:24:58 +0000
parents 86e52cd983ca
children
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1 <tool id="recetox_aplcms_compute_clusters" name="recetox-aplcms - compute clusters" version="@TOOL_VERSION@+galaxy2" profile="21.09">
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2 <description>compute clusters of mz and rt across samples and assign cluster IDs to individual features</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_2928</edam_operation>
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9 </edam_operations>
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10 <expand macro="annotation"/>
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11 <expand macro="creator"/>
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12 <expand macro="requirements"/>
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14 <command detect_errors="aggressive"><![CDATA[
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15 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
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16 ]]></command>
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17 <configfiles>
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18 <configfile name="run_script"><![CDATA[
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19 #set filenames = str("', '").join([str($f) for $f in $files])
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20 feature_tables <- load_parquet_collection(c('$filenames'))
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21 sample_names <- unlist(lapply(feature_tables, load_sample_name))
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23 validate_sample_names(sample_names)
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25 ordering <- order(sample_names)
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26 feature_tables <- feature_tables[ordering]
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27 sample_names <- sample_names[ordering]
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29 clusters <- compute_clusters_simple(
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30 feature_tables = feature_tables,
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31 sample_names = sample_names,
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32 mz_tol_ppm = $mz_tol_relative_ppm,
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33 rt_tol = $rt_tol
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34 )
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36 sample_names <- unlist(lapply(clusters, restore_sample_name))
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37 save_parquet_collection(clusters, sample_names, "clustered")
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38 ]]></configfile>
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39 </configfiles>
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41 <inputs>
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42 <param name="files" type="data_collection" collection_type="list" format="parquet" label="Input data"
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43 help="List of tables containing features." />
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44 <expand macro="tolerances"/>
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45 </inputs>
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47 <outputs>
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48 <collection name="clustered_feature_tables" type="list"
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49 label="${tool.name} feature_tables on ${on_string}">
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50 <discover_datasets pattern="__designation__" directory="clustered" format="parquet" />
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51 </collection>
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52 </outputs>
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54 <tests>
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56 </tests>
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58 <help>
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59 <![CDATA[
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60 @COMPUTE_CLUSTERS_HELP@
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62 @GENERAL_HELP@
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63 ]]>
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64 </help>
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66 <expand macro="citations"/>
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67 </tool>