Mercurial > repos > recetox > aplcms_unsupervised
annotate aplcms_unsupervised.xml @ 1:bcc9f27fea2b draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
author | recetox |
---|---|
date | Tue, 26 Jan 2021 17:10:34 +0000 |
parents | 7c80b743a2db |
children | 8c6dbef97001 |
rev | line source |
---|---|
1
bcc9f27fea2b
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
recetox
parents:
0
diff
changeset
|
1 <tool id="aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy2"> |
0
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
2 <macros> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
3 <import>aplcms_macros.xml</import> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
4 </macros> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
5 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
6 <expand macro="requirements" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
7 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
8 <command detect_errors="aggressive"><![CDATA[ |
1
bcc9f27fea2b
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
recetox
parents:
0
diff
changeset
|
9 #set file_str = str("', '").join([str($f) for $f in $files]) |
0
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
10 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
11 Rscript |
1
bcc9f27fea2b
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
recetox
parents:
0
diff
changeset
|
12 -e "x <- apLCMS::unsupervised( |
bcc9f27fea2b
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
recetox
parents:
0
diff
changeset
|
13 files = c('$file_str'), |
0
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
14 min_exp = $noise_filtering.min_exp, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
15 min_pres = $noise_filtering.min_pres, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
16 min_run = $noise_filtering.min_run, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
17 mz_tol = $noise_filtering.mz_tol, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
18 baseline_correct = $noise_filtering.baseline_correct, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
19 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
20 intensity_weighted = $noise_filtering.intensity_weighted, |
1
bcc9f27fea2b
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
recetox
parents:
0
diff
changeset
|
21 shape_model = '$feature_detection.shape_model', |
0
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
22 BIC_factor = $feature_detection.BIC_factor, |
1
bcc9f27fea2b
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
recetox
parents:
0
diff
changeset
|
23 peak_estim_method = '$feature_detection.peak_estim_method', |
0
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
24 min_bandwidth = $feature_detection.min_bandwidth, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
25 max_bandwidth = $feature_detection.max_bandwidth, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
26 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max), |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
27 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max), |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
28 component_eliminate = $feature_detection.component_eliminate, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
29 moment_power = $feature_detection.moment_power, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
30 align_chr_tol = $peak_alignment.align_chr_tol, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
31 align_mz_tol = $peak_alignment.align_mz_tol, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
32 max_align_mz_diff = $peak_alignment.max_align_mz_diff, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
33 recover_mz_range = $weak_signal_recovery.recover_mz_range, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
34 recover_chr_range = $weak_signal_recovery.recover_chr_range, |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
35 use_observed_range = $weak_signal_recovery.use_observed_range, |
1
bcc9f27fea2b
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
recetox
parents:
0
diff
changeset
|
36 recover_min_count = $weak_signal_recovery.recover_min_count, |
bcc9f27fea2b
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
recetox
parents:
0
diff
changeset
|
37 cluster = as.integer(\${GALAXY_SLOTS:-1}) |
bcc9f27fea2b
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
recetox
parents:
0
diff
changeset
|
38 )" |
bcc9f27fea2b
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
recetox
parents:
0
diff
changeset
|
39 -e "apLCMS::save_peaks_to_hdf('$peaks', x)" |
0
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
40 ]]></command> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
41 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
42 <expand macro="inputs"> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
43 <expand macro="noise_filtering" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
44 <expand macro="feature_detection" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
45 <expand macro="peak_alignment" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
46 <expand macro="weak_signal_recovery" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
47 </expand> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
48 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
49 <outputs> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
50 <data name="peaks" format="h5" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
51 </outputs> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
52 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
53 <tests> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
54 <test> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
55 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
56 <output name="peaks" file="peaks_unsupervised.h5" ftype="h5" compare="sim_size" delta="1000"/> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
57 </test> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
58 </tests> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
59 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
60 <help> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
61 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
62 any historically detected features. For such functionality please use the Hybrid version of apLCMS. |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
63 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
64 @GENERAL_HELP@ |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
65 </help> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
66 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
67 <expand macro="citations" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
parents:
diff
changeset
|
68 </tool> |