Mercurial > repos > recetox > recetox_aplcms_unsupervised

comparison aplcms_unsupervised.xml @ 1:52cec2e123fa draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
author recetox
date Thu, 24 Sep 2020 00:15:56 +0000
parents bfe186af3dca
children b0ba0287b76f
comparison
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0:bfe186af3dca 1:52cec2e123fa
1 <tool id="recetox_aplcms_unsupervised" name="apLCMS - Unsupervised" version="@VERSION@"> 1 <tool id="recetox_aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy0">
2 <macros> 2 <macros>
3 <import>aplcms_macros.xml</import> 3 <import>aplcms_macros.xml</import>
4 </macros> 4 </macros>
5 5
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 7
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 #set file_str = str('", "').join([str($f) for $f in $files]) 9 #set file_str = str('", "').join([str($f) for $f in $files])
10 10
11 Rscript 11 Rscript
12 -e 'result <- apLCMS::unsupervised( 12 -e 'x <- apLCMS::unsupervised(
13 files = c("$file_str"), 13 files = c("$file_str"),
14 min_exp = $noise_filtering.min_exp, 14 min_exp = $noise_filtering.min_exp,
15 min_pres = $noise_filtering.min_pres, 15 min_pres = $noise_filtering.min_pres,
16 min_run = $noise_filtering.min_run, 16 min_run = $noise_filtering.min_run,
17 mz_tol = $noise_filtering.mz_tol, 17 mz_tol = $noise_filtering.mz_tol,
33 recover_mz_range = $weak_signal_recovery.recover_mz_range, 33 recover_mz_range = $weak_signal_recovery.recover_mz_range,
34 recover_chr_range = $weak_signal_recovery.recover_chr_range, 34 recover_chr_range = $weak_signal_recovery.recover_chr_range,
35 use_observed_range = $weak_signal_recovery.use_observed_range, 35 use_observed_range = $weak_signal_recovery.use_observed_range,
36 recover_min_count = $weak_signal_recovery.recover_min_count 36 recover_min_count = $weak_signal_recovery.recover_min_count
37 )' 37 )'
38 -e 'arrow::write_feather(result\$final_times, "$times")' 38 -e 'rhdf5::h5write(x\$final_peaks, "$peaks", "peaks")'
39 -e 'arrow::write_feather(result\$final_features, "$features")' 39 -e 'rhdf5::h5write(x\$aligned_peaks, "$peaks", "aligned_peaks")'
40 -e 'arrow::write_feather(result\$aligned_times, "$aligned_times")' 40 -e 'rhdf5::h5write(x\$corrected_features, "$peaks", "corrected_features")'
41 -e 'arrow::write_feather(result\$aligned_features, "$aligned_features")' 41 -e 'rhdf5::h5write(x\$extracted_features, "$peaks", "extracted_features")'
42 -e 'arrow::write_feather(result\$corrected_features, "$corrected_features")' 42 -e 'rhdf5::h5write(x\$aligned_mz_tolerance, "$peaks", "aligned_mz_tolerance")'
43 -e 'arrow::write_feather(result\$extracted_features, "$extracted_features")' 43 -e 'rhdf5::h5write(x\$aligned_rt_tolerance, "$peaks", "aligned_rt_tolerance")'
44 ]]></command> 44 ]]></command>
45 45
46 <expand macro="inputs"> 46 <expand macro="inputs">
47 <expand macro="noise_filtering" /> 47 <expand macro="noise_filtering" />
48 <expand macro="feature_detection" /> 48 <expand macro="feature_detection" />
49 <expand macro="peak_alignment" /> 49 <expand macro="peak_alignment" />
50 <expand macro="weak_signal_recovery" /> 50 <expand macro="weak_signal_recovery" />
51 </expand> 51 </expand>
52 52
53 <outputs> 53 <outputs>
54 <data name="times" format="time_table.feather" /> 54 <data name="peaks" format="h5" />
55 <data name="features" format="peak_table.feather" />
56 <data name="aligned_times" format="time_table.feather" hidden="true" />
57 <data name="aligned_features" format="peak_table.feather" hidden="true" />
58 <data name="corrected_features" format="peak_table.feather" hidden="true" />
59 <data name="extracted_features" format="peak_table.feather" hidden="true" />
60 </outputs> 55 </outputs>
61 56
62 <help> 57 <help>
63 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or 58 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
64 any historically detected features. For such functionality please use the Hybrid version of apLCMS. 59 any historically detected features. For such functionality please use the Hybrid version of apLCMS.