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comparison 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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-1:000000000000 0:e5a53ff3f2ed
1 <tool id="recetox_aplcms_adjust_time" name="RECETOX apLCMS - adjust time" version="@TOOL_VERSION@+galaxy0">
2 <description>corrects the retention time of features from LC/MS spectra</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 $files
17 ln -s '${infile}' '${infile.element_identifier}'
18 #end for
19 </configfile>
20 <configfile name="run_script"><![CDATA[
21 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files])
22 extracted_features <- load_features(c('$filenames_str'))
23
24 corrected <- adjust.time(
25 features = extracted_features,
26 #if $peak_alignment.align_mz_tol:
27 mz.tol = $peak_alignment.align_mz_tol,
28 #end if
29 #if $peak_alignment.align_chr_tol:
30 chr.tol = $peak_alignment.align_chr_tol,
31 #end if
32 find.tol.max.d = 10 * $mz_tol,
33 max.align.mz.diff = $peak_alignment.max_align_mz_diff,
34 do.plot = FALSE
35 )
36
37 save_data_as_parquet_files(corrected, "corrected")
38 ]]></configfile>
39 </configfiles>
40
41 <inputs>
42 <param name="files" type="data" format="parquet" multiple="true" min="2" label="Input data"
43 help="Mass spectrometry sample-wise feature tables." />
44 <expand macro="mz_tol_macro"/>
45 <expand macro="peak_alignment"/>
46 </inputs>
47
48 <outputs>
49 <collection name="corrected_feature_tables" type="list"
50 label="${tool.name} corrected_feature_tables on ${on_string}">
51 <discover_datasets pattern="__designation__" directory="corrected" format="parquet" />
52 </collection>
53 </outputs>
54
55 <tests>
56 <test>
57 <param name="files" ftype="parquet"
58 value="extracted_expected/extracted_0.parquet,extracted_expected/extracted_1.parquet,extracted_expected/extracted_2.parquet"/>
59 <output_collection name="corrected_feature_tables" type="list">
60 <element name="corrected_features_0.parquet" file="corrected_expected/corrected_0.parquet" ftype="parquet"/>
61 <element name="corrected_features_1.parquet" file="corrected_expected/corrected_1.parquet" ftype="parquet"/>
62 <element name="corrected_features_2.parquet" file="corrected_expected/corrected_2.parquet" ftype="parquet"/>
63 </output_collection>
64 </test>
65 </tests>
66
67 <help>
68 <![CDATA[
69 This is a tool which runs apLCMS adjustment of retention times.
70
71 @GENERAL_HELP@
72 ]]>
73 </help>
74
75 <expand macro="citations"/>
76 </tool>