Mercurial > repos > recetox > recetox_aplcms_two_step_hybrid

annotate recetox_aplcms_two_step_hybrid.xml @ 1:87b669bdb51a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
author recetox
date Fri, 10 Jun 2022 10:15:47 +0000
parents c67f0eb6a909
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
1 <tool id="recetox_aplcms_two_step_hybrid" name="RECETOX apLCMS Two-Step Hybrid" version="@TOOL_VERSION@+galaxy0">
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
2 <description>generate a feature table from LC/MS spectra of multi-batch experiments</description>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
3 <macros>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
4 <import>macros.xml</import>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
5 </macros>
1
87b669bdb51a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents: 0
diff changeset
6 <expand macro="creator"/>
0
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
7
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
8 <expand macro="requirements"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
9 <command detect_errors="aggressive"><![CDATA[
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
10 sh ${symlink_inputs} &&
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
11 Rscript -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")'
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
12 ]]></command>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
13 <configfiles>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
14 <configfile name="symlink_inputs">
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
15 #for $infile in $files
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
16 ln -s '${infile}' '${infile.element_identifier}'
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
17 #end for
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
18 </configfile>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
19 <configfile name="run_script"><![CDATA[
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
20 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files])
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
21
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
22 two_step_hybrid_main(
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
23 sample_files = c('$filenames_str'),
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
24 known_table_file = '${known_table}',
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
25 updated_known_table_file = '${updated_known_table}',
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
26 recovered_file = '${recovered_feature_sample_table}',
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
27 aligned_file = '${aligned_feature_sample_table}',
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
28 out_format = '$output_format.out_format',
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
29 metadata = '${metadata}',
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
30 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1)),
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
31 min.within.batch.prop.detect = $multibatch_processing.min_within_batch_prop_detect,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
32 min.within.batch.prop.report = $multibatch_processing.min_within_batch_prop_detect,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
33 min.batch.prop = $multibatch_processing.min_batch_prop,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
34 batch.align.mz.tol = $multibatch_processing.batch_align_mz_tol,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
35 batch.align.chr.tol = $multibatch_processing.batch_align_chr_tol,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
36 min.pres = $noise_filtering.min_pres,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
37 min.run = $noise_filtering.min_run,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
38 mz.tol = $noise_filtering.mz_tol,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
39 baseline.correct.noise.percentile = $noise_filtering.baseline_correct_noise_percentile,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
40 baseline.correct = $noise_filtering.baseline_correct,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
41 intensity.weighted = $noise_filtering.intensity_weighted,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
42 shape.model = '$feature_detection.shape_model',
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
43 peak.estim.method = '$feature_detection.peak_estim_method',
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
44 BIC.factor = $feature_detection.BIC_factor,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
45 min.bw = $feature_detection.min_bandwidth,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
46 max.bw = $feature_detection.max_bandwidth,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
47 sd.cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
48 sigma.ratio.lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
49 component.eliminate = $feature_detection.component_eliminate,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
50 moment.power = $feature_detection.moment_power,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
51 align.mz.tol = $peak_alignment.align_mz_tol,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
52 align.chr.tol = $peak_alignment.align_chr_tol,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
53 max.align.mz.diff = $peak_alignment.max_align_mz_diff,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
54 recover.mz.range = $weak_signal_recovery.recover_mz_range,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
55 recover.chr.range = $weak_signal_recovery.recover_chr_range,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
56 use.observed.range = $weak_signal_recovery.use_observed_range,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
57 recover.min.count = $weak_signal_recovery.recover_min_count,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
58 match.tol.ppm = $history_db.match_tol_ppm,
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
59 new.feature.min.count = $history_db.new_feature_min_count
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
60 )
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
61 ]]></configfile>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
62 </configfiles>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
63
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
64 <expand macro="inputs">
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
65 <param name="metadata" type="data" format="csv" label="metadata" help="A csv table with two columns, where the first column contains sample names and the second batch labels for each sample."/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
66 <expand macro="history_db"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
67 <expand macro="noise_filtering" />
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
68 <expand macro="feature_detection"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
69 <expand macro="peak_alignment"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
70 <expand macro="weak_signal_recovery"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
71 <expand macro="multibatch_processing"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
72 <expand macro="output_format"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
73 </expand>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
74
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
75 <outputs>
1
87b669bdb51a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents: 0
diff changeset
76 <expand macro="unsupervised_outputs">
87b669bdb51a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents: 0
diff changeset
77 <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/>
87b669bdb51a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents: 0
diff changeset
78 </expand>
0
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
79 </outputs>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
80
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
81 <tests>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
82 <test>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
83 <param name="known_table" value="known_table.parquet" ftype="parquet"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
84 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml,mbr_test0_copy.mzml" ftype="mzml"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
85 <param name="metadata" value="two_step_hybrid_info.csv" ftype="csv"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
86 <param name="moment_power" value="2"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
87 <param name="sd_cut_max" value="100"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
88 <param name="sd_cut_min" value="0.1"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
89 <param name="sigma_ratio_lim_max" value="20"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
90 <param name="sigma_ratio_lim_min" value="0.05"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
91 <section name="output_format">
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
92 <param name="out_format" value="recetox"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
93 </section>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
94 <output name="recovered_feature_sample_table" file="two_step_hybrid.recetox.parquet" ftype="parquet"/>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
95 </test>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
96 </tests>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
97
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
98 <help>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
99 <![CDATA[
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
100 @HELP_two-step-hybrid@
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
101 ]]>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
102 </help>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
103
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
104 <expand macro="citations">
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
105 <citation type="doi">10.1038/s41598-020-70850-0</citation>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
106 </expand>
c67f0eb6a909 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
recetox
parents:
diff changeset
107 </tool>