Mercurial > repos > recetox > recetox_aplcms_extract_features

annotate recetox_aplcms_extract_features.xml @ 0:d78dc8992e5a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
author recetox
date Fri, 10 Jun 2022 10:17:01 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
1 <tool id="recetox_aplcms_extract_features" name="RECETOX apLCMS - extract features" version="@TOOL_VERSION@+galaxy0">
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
2 <description>extract features from LC/MS spectra</description>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
3 <macros>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
4 <import>macros.xml</import>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
5 <import>macros_split.xml</import>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
6 </macros>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
7 <expand macro="creator"/>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
8
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
9 <expand macro="requirements"/>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
10 <command detect_errors="aggressive"><![CDATA[
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
11 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
12 ]]></command>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
13 <configfiles>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
14 <configfile name="run_script"><![CDATA[
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
15 profile <- proc.cdf(
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
16 filename = "$file",
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
17 min.pres = $noise_filtering.min_pres,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
18 min.run = $noise_filtering.min_run,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
19 tol = $noise_filtering.mz_tol,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
20 baseline.correct = $noise_filtering.baseline_correct,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
21 baseline.correct.noise.percentile = $noise_filtering.baseline_correct_noise_percentile,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
22 intensity.weighted = $noise_filtering.intensity_weighted,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
23 do.plot = FALSE,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
24 cache = FALSE
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
25 )
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
26
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
27 features <- prof.to.features(
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
28 a = profile,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
29 min.bw = $feature_detection.min_bandwidth,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
30 max.bw = $feature_detection.max_bandwidth,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
31 sd.cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
32 sigma.ratio.lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
33 shape.model = '$feature_detection.shape_model',
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
34 estim.method = '$feature_detection.peak_estim_method',
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
35 component.eliminate = $feature_detection.component_eliminate,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
36 power = $feature_detection.moment_power,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
37 BIC.factor = $feature_detection.BIC_factor,
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
38 do.plot = FALSE
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
39 )
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
40
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
41 df <- as.data.frame(features)
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
42 arrow::write_parquet(df, "$feature_sample_table")
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
43 ]]></configfile>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
44 </configfiles>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
45
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
46 <inputs>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
47 <param name="file" type="data" format="mzdata,mzml,mzxml,netcdf" label="Input file"
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
48 help="Mass spectrometry file for peak extraction." />
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
49 <expand macro="noise_filtering_split"/>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
50 <expand macro="feature_detection"/>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
51 </inputs>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
52
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
53 <outputs>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
54 <data name="feature_sample_table" format="parquet" label="${tool.name} on ${on_string}" />
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
55 </outputs>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
56
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
57 <tests>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
58 <test>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
59 <param name="file" value="mbr_test0.mzml" ftype="mzml"/>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
60 <output name="feature_sample_table" file="extracted_expected/extracted_0.parquet" ftype="parquet"/>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
61 </test>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
62 <test>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
63 <param name="file" value="mbr_test1.mzml" ftype="mzml"/>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
64 <output name="feature_sample_table" file="extracted_expected/extracted_1.parquet" ftype="parquet"/>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
65 </test>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
66 <test>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
67 <param name="file" value="mbr_test2.mzml" ftype="mzml"/>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
68 <output name="feature_sample_table" file="extracted_expected/extracted_2.parquet" ftype="parquet"/>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
69 </test>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
70 </tests>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
71
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
72 <help>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
73 <![CDATA[
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
74 This is a tool which runs apLCMS features extraction.
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
75
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
76 @GENERAL_HELP@
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
77 ]]>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
78 </help>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
79
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
80 <expand macro="citations"/>
d78dc8992e5a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
81 </tool>