Mercurial > repos > recetox > mfassignr_findrecalseries

comparison mfassignr_findRecalSeries.xml @ 4:1b4881c150cc draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 7d98b78ae27b24ee581d40ff0b624d7ecb288030
author recetox
date Fri, 01 Nov 2024 08:19:40 +0000
parents ad4176b336dc
children
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3:18e13043167d 4:1b4881c150cc
10 <edam_operations> 10 <edam_operations>
11 <edam_operation>operation_3627</edam_operation> 11 <edam_operation>operation_3627</edam_operation>
12 </edam_operations> 12 </edam_operations>
13 <expand macro="creator" /> 13 <expand macro="creator" />
14 <expand macro="refs" /> 14 <expand macro="refs" />
15 <expand macro="requirements" />
15 16
16 <expand macro="requirements" />
17 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
18 Rscript -e 'packageVersion("MFAssignR")' && 18 Rscript -e 'packageVersion("MFAssignR")' &&
19 Rscript '${mfassignr_findrecalseries}' 19 Rscript '${mfassignr_findrecalseries}'
20 ]]> 20 ]]>
21 </command> 21 </command>
22
22 <configfiles> 23 <configfiles>
23 <configfile name="mfassignr_findrecalseries"><![CDATA[ 24 <configfile name="mfassignr_findrecalseries"><![CDATA[
24 library(dplyr) 25 library(dplyr)
25 df <- read.table("$input_file", header=TRUE, sep="\t") 26 df <- read.table("$input_file", header=TRUE, sep="\t")
26 result <- MFAssignR::FindRecalSeries( 27 result <- MFAssignR::FindRecalSeriesSimple(df) |> dplyr::slice(-1)
27 df = df,
28 global_min = $global_min,
29 global_max = $global_max,
30 number_of_combinations = $number_of_combinations,
31 abundance_score_threshold = $abundance_score_threshold,
32 peak_distance_threshold = $peak_distance_threshold,
33 coverage_threshold = $coverage_threshold,
34 fill_series = $fill_series
35 ) |> dplyr::rename(Series = series)
36
37 write.table(result, file="$final_series", sep="\t", row.names=FALSE) 28 write.table(result, file="$final_series", sep="\t", row.names=FALSE)
38 ]]></configfile> 29 ]]></configfile>
39 </configfiles> 30 </configfiles>
31
40 <inputs> 32 <inputs>
41 <expand macro="findrecalseries_param"/> 33 <param name="input_file" type="data" format="tabular" label="Input data"
34 help="Recalibration series, output from RecalList"/>
42 </inputs> 35 </inputs>
36
43 <outputs> 37 <outputs>
44 <data name="final_series" format="tabular" label="Final recalibration series"/> 38 <data name="final_series" format="tabular" label="Final recalibration series"/>
45 </outputs> 39 </outputs>
40
46 <tests> 41 <tests>
47 <test> 42 <test>
48 <param name="input_file" value="recallist/recal_series.tabular"/> 43 <param name="input_file" value="recallist/recal_series.tabular"/>
49 <param name="global_min" value="100"/> 44 <output name="final_series" file="findrecalseries/selected_series_simple.tabular"/>
50 <param name="global_max" value="500"/>
51 <param name="abundance_score_threshold" value="50"/>
52 <param name="number_of_combinations" value="3"/>
53 <param name="coverage_threshold" value="50"/>
54 <param name="fill_series" value="TRUE"/>
55 <output name="final_series" file="findrecalseries/selected_series.tabular"/>
56 </test> 45 </test>
57 </tests> 46 </tests>
47
58 <help> 48 <help>
59 @FINDRECALSERIES_HELP@ 49 @FINDRECALSERIES_HELP@
60 50
61 @GENERAL_HELP@ 51 @GENERAL_HELP@
62 </help> 52 </help>
53
63 <expand macro="citations"/> 54 <expand macro="citations"/>
64 </tool> 55 </tool>