Mercurial > repos > recetox > recetox_aplcms_align_features

annotate recetox_aplcms_align_features.xml @ 1:148327f1e1be draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 699355cdf45b2157e9eea3962a01950d469fb0ba
author recetox
date Thu, 16 Jun 2022 10:23:01 +0000
parents e867e0c90d29
children 4d1583e15960
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148327f1e1be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 699355cdf45b2157e9eea3962a01950d469fb0ba
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1 <tool id="recetox_aplcms_align_features" name="RECETOX apLCMS - align features" version="@TOOL_VERSION@+galaxy1">
0
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2 <description>align features from LC/MS spectra across samples</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>macros_split.xml</import>
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6 </macros>
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7 <expand macro="creator"/>
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8
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9 <expand macro="requirements"/>
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10 <command detect_errors="aggressive"><![CDATA[
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11 sh ${symlink_inputs} &&
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12 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
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13 ]]></command>
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14 <configfiles>
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15 <configfile name="symlink_inputs">
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16 #for $infile in $ms_files
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17 ln -s '${infile}' '${infile.element_identifier}'
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18 #end for
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19 #for $infile in $corrected_files
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20 ln -s '${infile}' '${infile.element_identifier}'
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21 #end for
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22 </configfile>
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23 <configfile name="run_script"><![CDATA[
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24 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $ms_files])
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25 files_list <- sort_samples_by_acquisition_number(c('$filenames_str'))
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26 sample_names <- get_sample_name(files_list)
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27
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28 #set corrected_files = str("', '").join([str($f.element_identifier) for $f in $corrected_files])
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29 corrected_features <- load_features(c('$corrected_files'))
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31 aligned <- align_features(
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32 sample_names = sample_names,
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33 features = corrected_features,
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34 min.exp = $min_exp,
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35 mz.tol = $peak_alignment.align_mz_tol,
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36 chr.tol = $peak_alignment.align_chr_tol,
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37 find.tol.max.d = 10 * $mz_tol,
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38 max.align.mz.diff = $peak_alignment.max_align_mz_diff,
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39 do.plot = FALSE
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40 )
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41
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42 save_aligned_features(aligned, "$rt_cross_table", "$int_cross_table", "$tolerances")
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43 ]]></configfile>
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44 </configfiles>
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45
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46 <inputs>
1
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47 <param name="ms_files" type="data_collection" collection_type="list" format="mzdata,mzml,mzxml,netcdf"
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48 label="Input data collection" help="Mass spectrometry file for peak extraction." />
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49 <param name="corrected_files" type="data_collection" collection_type="list" format="parquet"
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50 label="Input corrected feature samples collection"
0
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51 help="Mass spectrometry files containing corrected feature samples." />
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52 <expand macro="mz_tol_macro"/>
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53 <param name="min_exp" type="integer" min="1" value="2" label="min_exp"
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54 help="If a feature is to be included in the final feature table, it must be present in at least this number of spectra." />
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55 <expand macro="peak_alignment"/>
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56 </inputs>
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57
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58 <outputs>
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59 <data name="tolerances" format="parquet" label="${tool.name} on ${on_string} (tolerances)" />
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60 <data name="rt_cross_table" format="parquet" label="${tool.name} on ${on_string} (rt cross table)" />
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61 <data name="int_cross_table" format="parquet" label="${tool.name} on ${on_string} (int cross table)" />
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62 </outputs>
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63
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64 <tests>
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65 <test>
1
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66 <param name="ms_files">
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67 <collection type="list">
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68 <element name="mbr_test0.mzml" value="mbr_test0.mzml"/>
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69 <element name="mbr_test1.mzml" value="mbr_test1.mzml"/>
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70 <element name="mbr_test2.mzml" value="mbr_test2.mzml"/>
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71 </collection>
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72 </param>
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73 <param name="corrected_files">
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74 <collection type="list">
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75 <element name="corrected_features_0.parquet" value="corrected_expected/corrected_0.parquet"/>
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76 <element name="corrected_features_1.parquet" value="corrected_expected/corrected_1.parquet"/>
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77 <element name="corrected_features_2.parquet" value="corrected_expected/corrected_2.parquet"/>
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78 </collection>
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79 </param>
0
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80 <output name="tolerances" file="tolerances.parquet" ftype="parquet"/>
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81 <output name="rt_cross_table" file="rt_cross_table.parquet" ftype="parquet"/>
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82 <output name="int_cross_table" file="int_cross_table.parquet" ftype="parquet"/>
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83 </test>
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84 </tests>
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85
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86 <help>
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87 <![CDATA[
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88 This is a tool which runs apLCMS alignment of features.
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89
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90 @GENERAL_HELP@
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91 ]]>
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92 </help>
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93
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94 <expand macro="citations"/>
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95 </tool>