Mercurial > repos > recetox > aplcms_unsupervised
annotate aplcms_unsupervised.xml @ 2:8c6dbef97001 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
author | recetox |
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date | Mon, 19 Apr 2021 12:26:57 +0000 |
parents | bcc9f27fea2b |
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rev | line source |
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2
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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1 <tool id="aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy3"> |
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7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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2 <macros> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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3 <import>aplcms_macros.xml</import> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
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4 </macros> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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5 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
recetox
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6 <expand macro="requirements" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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7 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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8 <command detect_errors="aggressive"><![CDATA[ |
2
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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9 Rscript ${run_script} |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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10 ]]></command> |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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11 |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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12 <configfiles> |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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13 <configfile name="run_script"><![CDATA[ |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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14 #set file_str = str("', '").join([str($f) for $f in $files]) |
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7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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15 |
2
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
recetox
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16 x <- apLCMS::unsupervised( |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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17 files = c('$file_str'), |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
recetox
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18 min_exp = $noise_filtering.min_exp, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
recetox
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19 min_pres = $noise_filtering.min_pres, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
recetox
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20 min_run = $noise_filtering.min_run, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
recetox
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21 mz_tol = $noise_filtering.mz_tol, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
recetox
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22 baseline_correct = $noise_filtering.baseline_correct, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
recetox
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23 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
recetox
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24 intensity_weighted = $noise_filtering.intensity_weighted, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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25 shape_model = '$feature_detection.shape_model', |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
recetox
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26 BIC_factor = $feature_detection.BIC_factor, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
recetox
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27 peak_estim_method = '$feature_detection.peak_estim_method', |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
recetox
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28 min_bandwidth = $feature_detection.min_bandwidth, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
recetox
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29 max_bandwidth = $feature_detection.max_bandwidth, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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30 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max), |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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31 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max), |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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32 component_eliminate = $feature_detection.component_eliminate, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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33 moment_power = $feature_detection.moment_power, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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34 align_chr_tol = $peak_alignment.align_chr_tol, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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35 align_mz_tol = $peak_alignment.align_mz_tol, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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36 max_align_mz_diff = $peak_alignment.max_align_mz_diff, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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37 recover_mz_range = $weak_signal_recovery.recover_mz_range, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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38 recover_chr_range = $weak_signal_recovery.recover_chr_range, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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39 use_observed_range = $weak_signal_recovery.use_observed_range, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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40 recover_min_count = $weak_signal_recovery.recover_min_count, |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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41 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1)) |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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42 ) |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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43 |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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44 apLCMS::save_peaks_to_hdf('$peaks', x) |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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45 ]]></configfile> |
8c6dbef97001
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
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46 </configfiles> |
0
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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47 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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48 <expand macro="inputs"> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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49 <expand macro="noise_filtering" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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50 <expand macro="feature_detection" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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51 <expand macro="peak_alignment" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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52 <expand macro="weak_signal_recovery" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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53 </expand> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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54 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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55 <outputs> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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56 <data name="peaks" format="h5" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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57 </outputs> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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58 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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59 <tests> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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60 <test> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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61 <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"
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62 <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"
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63 </test> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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64 </tests> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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65 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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66 <help> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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67 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"
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68 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"
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69 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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70 @GENERAL_HELP@ |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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71 </help> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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72 |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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73 <expand macro="citations" /> |
7c80b743a2db
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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74 </tool> |