Mercurial > repos > recetox > recetox_aplcms_remove_noise

comparison recetox_aplcms_remove_noise.xml @ 2:caa39ec7a18b draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
author recetox
date Wed, 24 May 2023 14:49:19 +0000
parents e9e9677e8147
children e3acbc988e14
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1:e9e9677e8147 2:caa39ec7a18b
13 ]]></command> 13 ]]></command>
14 <configfiles> 14 <configfiles>
15 <configfile name="run_script"><![CDATA[ 15 <configfile name="run_script"><![CDATA[
16 sample_name <- readChar('sample_name.txt', file.info('sample_name.txt')\$size) 16 sample_name <- readChar('sample_name.txt', file.info('sample_name.txt')\$size)
17 17
18 profile <- proc.cdf( 18 profile <- remove_noise(
19 filename = '$input_file', 19 filename = '$input_file',
20 min_pres = $min_pres, 20 min_pres = $min_pres,
21 min_run = $min_run, 21 min_run = $min_run,
22 mz_tol = $mz_tol/1e6, 22 mz_tol = ${mz_tol}/1e6,
23 baseline_correct = $baseline_correct, 23 baseline_correct = $baseline_correct,
24 baseline_correct_noise_percentile = 0.05, 24 baseline_correct_noise_percentile = 0.05,
25 intensity_weighted = $intensity_weighted, 25 intensity_weighted = $intensity_weighted,
26 do.plot = FALSE, 26 do.plot = FALSE,
27 cache = FALSE 27 cache = FALSE
41 <outputs> 41 <outputs>
42 <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" /> 42 <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" />
43 </outputs> 43 </outputs>
44 44
45 <tests> 45 <tests>
46 46 <test>
47 <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/>
48 <output name="output_file" file="remove_noise_docker.parquet" ftype="parquet" />
49 </test>
47 </tests> 50 </tests>
48 51
49 <help> 52 <help>
50 <![CDATA[ 53 <![CDATA[
51 @REMOVE_NOISE_HELP@ 54 @REMOVE_NOISE_HELP@