Mercurial > repos > recetox > recetox_aplcms_adjust_time

annotate recetox_aplcms_adjust_time.xml @ 0:e5a53ff3f2ed draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
author recetox
date Fri, 10 Jun 2022 10:16:23 +0000
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children 18eadec69334
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e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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1 <tool id="recetox_aplcms_adjust_time" name="RECETOX apLCMS - adjust time" version="@TOOL_VERSION@+galaxy0">
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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2 <description>corrects the retention time of features from LC/MS spectra</description>
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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3 <macros>
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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4 <import>macros.xml</import>
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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5 <import>macros_split.xml</import>
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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6 </macros>
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7 <expand macro="creator"/>
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8
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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9 <expand macro="requirements"/>
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10 <command detect_errors="aggressive"><![CDATA[
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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11 sh ${symlink_inputs} &&
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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12 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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13 ]]></command>
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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14 <configfiles>
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15 <configfile name="symlink_inputs">
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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16 #for $infile in $files
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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17 ln -s '${infile}' '${infile.element_identifier}'
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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18 #end for
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19 </configfile>
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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20 <configfile name="run_script"><![CDATA[
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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21 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files])
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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22 extracted_features <- load_features(c('$filenames_str'))
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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23
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24 corrected <- adjust.time(
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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25 features = extracted_features,
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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26 #if $peak_alignment.align_mz_tol:
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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27 mz.tol = $peak_alignment.align_mz_tol,
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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28 #end if
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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29 #if $peak_alignment.align_chr_tol:
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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30 chr.tol = $peak_alignment.align_chr_tol,
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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31 #end if
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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32 find.tol.max.d = 10 * $mz_tol,
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33 max.align.mz.diff = $peak_alignment.max_align_mz_diff,
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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34 do.plot = FALSE
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35 )
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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36
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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37 save_data_as_parquet_files(corrected, "corrected")
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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38 ]]></configfile>
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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39 </configfiles>
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40
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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41 <inputs>
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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42 <param name="files" type="data" format="parquet" multiple="true" min="2" label="Input data"
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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43 help="Mass spectrometry sample-wise feature tables." />
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44 <expand macro="mz_tol_macro"/>
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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45 <expand macro="peak_alignment"/>
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46 </inputs>
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47
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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48 <outputs>
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49 <collection name="corrected_feature_tables" type="list"
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50 label="${tool.name} corrected_feature_tables on ${on_string}">
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51 <discover_datasets pattern="__designation__" directory="corrected" format="parquet" />
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52 </collection>
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53 </outputs>
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54
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55 <tests>
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56 <test>
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57 <param name="files" ftype="parquet"
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58 value="extracted_expected/extracted_0.parquet,extracted_expected/extracted_1.parquet,extracted_expected/extracted_2.parquet"/>
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59 <output_collection name="corrected_feature_tables" type="list">
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60 <element name="corrected_features_0.parquet" file="corrected_expected/corrected_0.parquet" ftype="parquet"/>
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61 <element name="corrected_features_1.parquet" file="corrected_expected/corrected_1.parquet" ftype="parquet"/>
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62 <element name="corrected_features_2.parquet" file="corrected_expected/corrected_2.parquet" ftype="parquet"/>
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63 </output_collection>
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64 </test>
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65 </tests>
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66
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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67 <help>
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68 <![CDATA[
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69 This is a tool which runs apLCMS adjustment of retention times.
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70
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71 @GENERAL_HELP@
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72 ]]>
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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73 </help>
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74
e5a53ff3f2ed planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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75 <expand macro="citations"/>
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76 </tool>