Mercurial > repos > recetox > recetox_aplcms_align_features

annotate recetox_aplcms_align_features.xml @ 9:7b42ee54d757 draft

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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 00:27:03 +0000
parents 2d13fcae8b84
children 2b6bfa234d8b
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1 <tool id="recetox_aplcms_align_features" name="recetox-aplcms - align features" version="@TOOL_VERSION@+galaxy1" profile="21.09">
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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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8 <edam_operations>
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9 <edam_operation>operation_2928</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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16 <command detect_errors="aggressive"><![CDATA[
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17 Rscript -e "cluster <- \${GALAXY_SLOTS:-1}" -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
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18 ]]></command>
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19 <configfiles>
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20 <configfile name="run_script"><![CDATA[
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21 #set filenames = str("', '").join([str($f) for $f in $files])
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22 feature_tables <- load_parquet_collection(c('$filenames'))
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23 sample_names <- unlist(lapply(feature_tables, load_sample_name))
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25 validate_sample_names(sample_names)
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27 ordering <- order(sample_names)
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28 feature_tables <- feature_tables[ordering]
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29 sample_names <- sample_names[ordering]
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31 aligned_features <- create_aligned_feature_table(
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32 features_table = dplyr::bind_rows(feature_tables),
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33 min_occurrence = $min_occurrence,
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34 sample_names = sample_names,
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35 mz_tol_relative = $mz_tol_relative_ppm * 1e-06,
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36 rt_tol_relative = $rt_tol,
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37 cluster = cluster
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38 )
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40 save_aligned_features(aligned_features, '$metadata_file', '$rt_file', '$intensity_file')
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41 ]]></configfile>
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42 </configfiles>
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44 <inputs>
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45 <param name="files" type="data_collection" collection_type="list" format="parquet"
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46 label="Clustered features" help="List of tables containing clustered features." />
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47 <expand macro="tolerances"/>
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48 <param name="min_occurrence" type="integer" min="2" value="2" label="Minimal occurrence in samples"
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49 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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50 </inputs>
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52 <outputs>
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53 <data name="metadata_file" format="parquet" label="${tool.name} on ${on_string} (metadata table)"/>
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54 <data name="rt_file" format="parquet" label="${tool.name} on ${on_string} (rt table)"/>
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55 <data name="intensity_file" format="parquet" label="${tool.name} on ${on_string} (intensity table)"/>
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56 </outputs>
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58 <tests>
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59
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60 </tests>
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62 <help>
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63 <![CDATA[
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64 @ALIGN_FEATURES_HELP@
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66 @GENERAL_HELP@
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67 ]]>
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68 </help>
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70 <expand macro="citations"/>
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71 </tool>