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comparison recetox_aplcms_extract_features.xml @ 0:63a41aa211e1 draft default tip

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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 10:12:38 +0000
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1 <tool id="recetox_aplcms_extract_features" name="RECETOX apLCMS - extract features" version="@TOOL_VERSION@+galaxy0">
2 <description>extract 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 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
12 ]]></command>
13 <configfiles>
14 <configfile name="run_script"><![CDATA[
15 profile <- proc.cdf(
16 filename = "$file",
17 min.pres = $noise_filtering.min_pres,
18 min.run = $noise_filtering.min_run,
19 tol = $noise_filtering.mz_tol,
20 baseline.correct = $noise_filtering.baseline_correct,
21 baseline.correct.noise.percentile = $noise_filtering.baseline_correct_noise_percentile,
22 intensity.weighted = $noise_filtering.intensity_weighted,
23 do.plot = FALSE,
24 cache = FALSE
25 )
26
27 features <- prof.to.features(
28 a = profile,
29 min.bw = $feature_detection.min_bandwidth,
30 max.bw = $feature_detection.max_bandwidth,
31 sd.cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
32 sigma.ratio.lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
33 shape.model = '$feature_detection.shape_model',
34 estim.method = '$feature_detection.peak_estim_method',
35 component.eliminate = $feature_detection.component_eliminate,
36 power = $feature_detection.moment_power,
37 BIC.factor = $feature_detection.BIC_factor,
38 do.plot = FALSE
39 )
40
41 df <- as.data.frame(features)
42 arrow::write_parquet(df, "$feature_sample_table")
43 ]]></configfile>
44 </configfiles>
45
46 <inputs>
47 <param name="file" type="data" format="mzdata,mzml,mzxml,netcdf" label="Input file"
48 help="Mass spectrometry file for peak extraction." />
49 <expand macro="noise_filtering_split"/>
50 <expand macro="feature_detection"/>
51 </inputs>
52
53 <outputs>
54 <data name="feature_sample_table" format="parquet" label="${tool.name} on ${on_string}" />
55 </outputs>
56
57 <tests>
58 <test>
59 <param name="file" value="mbr_test0.mzml" ftype="mzml"/>
60 <output name="feature_sample_table" file="extracted_expected/extracted_0.parquet" ftype="parquet"/>
61 </test>
62 <test>
63 <param name="file" value="mbr_test1.mzml" ftype="mzml"/>
64 <output name="feature_sample_table" file="extracted_expected/extracted_1.parquet" ftype="parquet"/>
65 </test>
66 <test>
67 <param name="file" value="mbr_test2.mzml" ftype="mzml"/>
68 <output name="feature_sample_table" file="extracted_expected/extracted_2.parquet" ftype="parquet"/>
69 </test>
70 </tests>
71
72 <help>
73 <![CDATA[
74 This is a tool which runs apLCMS features extraction.
75
76 @GENERAL_HELP@
77 ]]>
78 </help>
79
80 <expand macro="citations"/>
81 </tool>