Mercurial > repos > recetox > recetox_aplcms_unsupervised

comparison aplcms_unsupervised.xml @ 3:b0ba0287b76f 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 16:06:54 +0000
parents 52cec2e123fa
children
comparison
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2:3c2a4d95fe06 3:b0ba0287b76f
1 <tool id="recetox_aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="recetox_aplcms_unsupervised" name="apLCMS - Unsupervised" 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" />
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 = $weak_signal_recovery.recover_min_count
37 )' 37 )'
38 -e 'rhdf5::h5write(x\$final_peaks, "$peaks", "peaks")' 38 -e 'apLCMS::save_peaks_to_hdf("$peaks", x)'
39 -e 'rhdf5::h5write(x\$aligned_peaks, "$peaks", "aligned_peaks")'
40 -e 'rhdf5::h5write(x\$corrected_features, "$peaks", "corrected_features")'
41 -e 'rhdf5::h5write(x\$extracted_features, "$peaks", "extracted_features")'
42 -e 'rhdf5::h5write(x\$aligned_mz_tolerance, "$peaks", "aligned_mz_tolerance")'
43 -e 'rhdf5::h5write(x\$aligned_rt_tolerance, "$peaks", "aligned_rt_tolerance")'
44 ]]></command> 39 ]]></command>
45 40
46 <expand macro="inputs"> 41 <expand macro="inputs">
47 <expand macro="noise_filtering" /> 42 <expand macro="noise_filtering" />
48 <expand macro="feature_detection" /> 43 <expand macro="feature_detection" />
52 47
53 <outputs> 48 <outputs>
54 <data name="peaks" format="h5" /> 49 <data name="peaks" format="h5" />
55 </outputs> 50 </outputs>
56 51
52 <tests>
53 <test>
54 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
55 <output name="peaks" file="peaks_unsupervised.h5" ftype="h5" compare="sim_size" delta="1000"/>
56 </test>
57 </tests>
58
57 <help> 59 <help>
58 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or 60 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
59 any historically detected features. For such functionality please use the Hybrid version of apLCMS. 61 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
60 62
61 @GENERAL_HELP@ 63 @GENERAL_HELP@