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comparison recetox_aplcms_align_features.xml @ 2:abe783e0daca draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
author recetox
date Mon, 13 Feb 2023 10:26:59 +0000
parents b07fd3d7ffd0
children 1e2a13bcb5a7
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1:b07fd3d7ffd0 2:abe783e0daca
1 <tool id="recetox_aplcms_align_features" name="RECETOX apLCMS - align features" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="recetox_aplcms_align_features" name="recetox-aplcms - align features" version="@TOOL_VERSION@+galaxy0">
2 <description>align features from LC/MS spectra across samples</description> 2 <description>align peaks across samples</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <import>macros_split.xml</import> 5 <import>help.xml</import>
6 </macros> 6 </macros>
7 <expand macro="creator"/> 7 <expand macro="creator"/>
8 <expand macro="requirements"/>
8 9
9 <expand macro="requirements"/>
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 sh ${symlink_inputs} &&
12 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' 11 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
13 ]]></command> 12 ]]></command>
14 <configfiles> 13 <configfiles>
15 <configfile name="symlink_inputs">
16 #for $infile in $ms_files
17 ln -s '${infile}' '${infile.element_identifier}'
18 #end for
19 #for $infile in $corrected_files
20 ln -s '${infile}' '${infile.element_identifier}'
21 #end for
22 </configfile>
23 <configfile name="run_script"><![CDATA[ 14 <configfile name="run_script"><![CDATA[
24 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $ms_files]) 15 #set filenames = str("', '").join([str($f) for $f in $files])
25 files_list <- sort_samples_by_acquisition_number(c('$filenames_str')) 16 feature_tables <- load_parquet_collection(c('$filenames'))
26 sample_names <- get_sample_name(files_list) 17 sample_names <- unlist(lapply(feature_tables, load_sample_name))
27 18
28 #set corrected_files = str("', '").join([str($f.element_identifier) for $f in $corrected_files]) 19 validate_sample_names(sample_names)
29 corrected_features <- load_features(c('$corrected_files'))
30 20
31 aligned <- align_features( 21 ordering <- order(sample_names)
32 sample_names = sample_names, 22 feature_tables <- feature_tables[ordering]
33 features = corrected_features, 23 sample_names <- sample_names[ordering]
34 min.exp = $min_exp,
35 mz.tol = $peak_alignment.align_mz_tol,
36 chr.tol = $peak_alignment.align_chr_tol,
37 find.tol.max.d = 10 * $mz_tol,
38 max.align.mz.diff = $peak_alignment.max_align_mz_diff,
39 do.plot = FALSE
40 )
41 24
42 save_aligned_features(aligned, "$rt_cross_table", "$int_cross_table", "$tolerances") 25 tolerances <- load_data_from_parquet_file('$input_tolerances')
26
27 aligned_features <- create_aligned_feature_table(
28 features_table = dplyr::bind_rows(feature_tables),
29 min_occurrence = $min_occurrence,
30 sample_names = sample_names,
31 mz_tol_relative = get_mz_tol(tolerances),
32 rt_tol_relative = get_rt_tol(tolerances)
33 )
34
35 save_aligned_features(aligned_features, '$metadata_file', '$rt_file', '$intensity_file')
43 ]]></configfile> 36 ]]></configfile>
44 </configfiles> 37 </configfiles>
45 38
46 <inputs> 39 <inputs>
47 <param name="ms_files" type="data_collection" collection_type="list" format="mzdata,mzml,mzxml,netcdf" 40 <param name="files" type="data_collection" collection_type="list" format="parquet"
48 label="Input data collection" help="Mass spectrometry file for peak extraction." /> 41 label="Clustered features" help="List of tables containing clustered features." />
49 <param name="corrected_files" type="data_collection" collection_type="list" format="parquet" 42 <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet"
50 label="Input corrected feature samples collection" 43 help="Table containing tolerance values." />
51 help="Mass spectrometry files containing corrected feature samples." /> 44 <param name="min_occurrence" type="integer" min="2" value="2" label="min_occurrence"
52 <expand macro="mz_tol_macro"/> 45 help="A feature has to show up in at least this number of profiles to be included in the final result." />
53 <param name="min_exp" type="integer" min="1" value="2" label="min_exp"
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." />
55 <expand macro="peak_alignment"/>
56 </inputs> 46 </inputs>
57 47
58 <outputs> 48 <outputs>
59 <data name="tolerances" format="parquet" label="${tool.name} on ${on_string} (tolerances)" /> 49 <data name="metadata_file" format="parquet" label="${tool.name} on ${on_string} (metadata table)"/>
60 <data name="rt_cross_table" format="parquet" label="${tool.name} on ${on_string} (rt cross table)" /> 50 <data name="rt_file" format="parquet" label="${tool.name} on ${on_string} (rt table)"/>
61 <data name="int_cross_table" format="parquet" label="${tool.name} on ${on_string} (int cross table)" /> 51 <data name="intensity_file" format="parquet" label="${tool.name} on ${on_string} (intensity table)"/>
62 </outputs> 52 </outputs>
63 53
64 <tests> 54 <tests>
65 <test> 55
66 <param name="ms_files">
67 <collection type="list">
68 <element name="mbr_test0.mzml" value="mbr_test0.mzml"/>
69 <element name="mbr_test1.mzml" value="mbr_test1.mzml"/>
70 <element name="mbr_test2.mzml" value="mbr_test2.mzml"/>
71 </collection>
72 </param>
73 <param name="corrected_files">
74 <collection type="list">
75 <element name="corrected_features_0.parquet" value="corrected_expected/corrected_0.parquet"/>
76 <element name="corrected_features_1.parquet" value="corrected_expected/corrected_1.parquet"/>
77 <element name="corrected_features_2.parquet" value="corrected_expected/corrected_2.parquet"/>
78 </collection>
79 </param>
80 <output name="tolerances" file="tolerances.parquet" ftype="parquet"/>
81 <output name="rt_cross_table" file="rt_cross_table.parquet" ftype="parquet"/>
82 <output name="int_cross_table" file="int_cross_table.parquet" ftype="parquet"/>
83 </test>
84 </tests> 56 </tests>
85 57
86 <help> 58 <help>
87 <![CDATA[ 59 <![CDATA[
88 This is a tool which runs apLCMS alignment of features. 60 @ALIGN_FEATURES_HELP@
89 61
90 @GENERAL_HELP@ 62 @GENERAL_HELP@
91 ]]> 63 ]]>
92 </help> 64 </help>
93 65