Mercurial > repos > recetox > recetox_aplcms_align_features

comparison recetox_aplcms_align_features.xml @ 0:57c644d3f24c 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 10:17:46 +0000
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-1:000000000000 0:57c644d3f24c
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>
3 <macros>
4 <import>macros.xml</import>
5 <import>macros_split.xml</import>
6 </macros>
7 <expand macro="creator"/>
8
9 <expand macro="requirements"/>
10 <command detect_errors="aggressive"><![CDATA[
11 sh ${symlink_inputs} &&
12 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
13 ]]></command>
14 <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}' '${infile.element_identifier}'
21 #end for
22 </configfile>
23 <configfile name="run_script"><![CDATA[
24 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $ms_files])
25 files_list <- sort_samples_by_acquisition_number(c('$filenames_str'))
26 sample_names <- get_sample_name(files_list)
27
28 #set corrected_files = str("', '").join([str($f.element_identifier) for $f in $corrected_files])
29 corrected_features <- load_features(c('$corrected_files'))
30
31 aligned <- align_features(
32 sample_names = sample_names,
33 features = corrected_features,
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 = $peak_alignment.max_align_mz_diff,
39 do.plot = FALSE
40 )
41
42 save_aligned_features(aligned, "$rt_cross_table", "$int_cross_table", "$tolerances")
43 ]]></configfile>
44 </configfiles>
45
46 <inputs>
47 <param name="ms_files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="2" label="Input data"
48 help="Mass spectrometry file for peak extraction." />
49 <param name="corrected_files" type="data" format="parquet" multiple="true" min="2"
50 label="Input corrected feature samples"
51 help="Mass spectrometry files containing corrected feature samples." />
52 <expand macro="mz_tol_macro"/>
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>
57
58 <outputs>
59 <data name="tolerances" format="parquet" label="${tool.name} on ${on_string} (tolerances)" />
60 <data name="rt_cross_table" format="parquet" label="${tool.name} on ${on_string} (rt cross table)" />
61 <data name="int_cross_table" format="parquet" label="${tool.name} on ${on_string} (int cross table)" />
62 </outputs>
63
64 <tests>
65 <test>
66 <param name="ms_files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
67 <param name="corrected_files" ftype="parquet"
68 value="corrected_expected/corrected_0.parquet,corrected_expected/corrected_1.parquet,corrected_expected/corrected_2.parquet"/>
69 <output name="tolerances" file="tolerances.parquet" ftype="parquet"/>
70 <output name="rt_cross_table" file="rt_cross_table.parquet" ftype="parquet"/>
71 <output name="int_cross_table" file="int_cross_table.parquet" ftype="parquet"/>
72 </test>
73 </tests>
74
75 <help>
76 <![CDATA[
77 This is a tool which runs apLCMS alignment of features.
78
79 @GENERAL_HELP@
80 ]]>
81 </help>
82
83 <expand macro="citations"/>
84 </tool>