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comparison recetox_aplcms_remove_noise.xml @ 0:9b7ebb837477 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 10:24:57 +0000
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children 1eafdef0c141
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-1:000000000000 0:9b7ebb837477
1 <tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy0">
2 <description>filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>help.xml</import>
6 </macros>
7 <expand macro="creator"/>
8 <expand macro="requirements"/>
9
10 <command detect_errors="aggressive"><![CDATA[
11 python '${__tool_directory__}/mzml_id_getter.py' '$input_file';
12 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
13 ]]></command>
14 <configfiles>
15 <configfile name="run_script"><![CDATA[
16 sample_name <- readChar('sample_name.txt', file.info('sample_name.txt')\$size)
17
18 profile <- proc.cdf(
19 filename = '$input_file',
20 min_pres = $min_pres,
21 min_run = $min_run,
22 mz_tol = $mz_tol,
23 baseline_correct = $baseline_correct,
24 baseline_correct_noise_percentile = 0.05,
25 intensity_weighted = $intensity_weighted,
26 do.plot = FALSE,
27 cache = FALSE
28 )
29
30 profile <- save_sample_name(profile, sample_name)
31 save_data_as_parquet_file(profile, '$output_file')
32 ]]></configfile>
33 </configfiles>
34
35 <inputs>
36 <param label="Input spectra data" name="input_file" type="data" format="mzml"
37 help="Sample data in .mzml format acquired in profile mode." />
38 <expand macro="remove_noise_params"/>
39 </inputs>
40
41 <outputs>
42 <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" />
43 </outputs>
44
45 <tests>
46
47 </tests>
48
49 <help>
50 <![CDATA[
51 @REMOVE_NOISE_HELP@
52
53 @GENERAL_HELP@
54 ]]>
55 </help>
56
57 <expand macro="citations"/>
58 </tool>