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comparison aplcms_hybrid.xml @ 3:bb4ffaeba411 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 1852a90740a2e1e98f576d68164100c46daaf71a"
author recetox
date Wed, 07 Oct 2020 16:07:23 +0000
parents 30b1888f985a
children
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2:ec8d56a91335 3:bb4ffaeba411
1 <tool id="recetox_aplcms_hybrid" name="apLCMS - Hybrid" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="recetox_aplcms_hybrid" name="apLCMS - Hybrid" version="@TOOL_VERSION@+galaxy1">
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" />
9 #set file_str = str('", "').join([str($f) for $f in $files]) 9 #set file_str = str('", "').join([str($f) for $f in $files])
10 10
11 Rscript 11 Rscript
12 -e 'x <- apLCMS::hybrid( 12 -e 'x <- apLCMS::hybrid(
13 files = c("$file_str"), 13 files = c("$file_str"),
14 known_table = rhdf5::h5read("$known_table", "aplcms_known_table"), 14 known_table = apLCMS::load_known_table_from_hdf("$known_table"),
15 min_exp = $noise_filtering.min_exp, 15 min_exp = $noise_filtering.min_exp,
16 min_pres = $noise_filtering.min_pres, 16 min_pres = $noise_filtering.min_pres,
17 min_run = $noise_filtering.min_run, 17 min_run = $noise_filtering.min_run,
18 mz_tol = $noise_filtering.mz_tol, 18 mz_tol = $noise_filtering.mz_tol,
19 baseline_correct = $noise_filtering.baseline_correct, 19 baseline_correct = $noise_filtering.baseline_correct,
36 recover_mz_range = $weak_signal_recovery.recover_mz_range, 36 recover_mz_range = $weak_signal_recovery.recover_mz_range,
37 recover_chr_range = $weak_signal_recovery.recover_chr_range, 37 recover_chr_range = $weak_signal_recovery.recover_chr_range,
38 use_observed_range = $weak_signal_recovery.use_observed_range, 38 use_observed_range = $weak_signal_recovery.use_observed_range,
39 recover_min_count = $weak_signal_recovery.recover_min_count 39 recover_min_count = $weak_signal_recovery.recover_min_count
40 )' 40 )'
41 -e 'rhdf5::h5write(x\$final_peaks, "$peaks", "peaks")' 41 -e 'apLCMS::save_peaks_to_hdf("$peaks", x)'
42 -e 'rhdf5::h5write(x\$aligned_peaks, "$peaks", "aligned_peaks")' 42 -e 'apLCMS::save_known_table_to_hdf("$updated_known_table", x\$updated_known_table)'
43 -e 'rhdf5::h5write(x\$corrected_features, "$peaks", "corrected_features")'
44 -e 'rhdf5::h5write(x\$extracted_features, "$peaks", "extracted_features")'
45 -e 'rhdf5::h5write(x\$aligned_mz_tolerance, "$peaks", "aligned_mz_tolerance")'
46 -e 'rhdf5::h5write(x\$aligned_rt_tolerance, "$peaks", "aligned_rt_tolerance")'
47 -e 'rhdf5::h5write(x\$updated_known_table, "$updated_known_table", "aplcms_known_table")'
48 ]]></command> 43 ]]></command>
49 44
50 <expand macro="inputs"> 45 <expand macro="inputs">
51 <expand macro="history_db" /> 46 <expand macro="history_db" />
52 <expand macro="noise_filtering" /> 47 <expand macro="noise_filtering" />
58 <outputs> 53 <outputs>
59 <data name="peaks" format="h5" /> 54 <data name="peaks" format="h5" />
60 <data name="updated_known_table" format="h5" /> 55 <data name="updated_known_table" format="h5" />
61 </outputs> 56 </outputs>
62 57
58 <tests>
59 <test>
60 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
61 <param name="known_table" value="known_table.h5" ftype="h5"/>
62 <output name="peaks" file="peaks_hybrid.h5" ftype="h5" compare="sim_size" delta="1000"/>
63 </test>
64 </tests>
65
63 <help> 66 <help>
64 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically 67 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
65 detected features on the same machinery to help detect and quantify lower-intensity peaks. 68 detected features on the same machinery to help detect and quantify lower-intensity peaks.
66 69
67 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography 70 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography