Mercurial > repos > recetox > recetox_aplcms_unsupervised

comparison recetox_aplcms_unsupervised.xml @ 11:e0f77e03599e draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:26:05 +0000
parents 6057540f65a9
children 6eeeebc35909
comparison
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10:6057540f65a9 11:e0f77e03599e
1 <tool id="recetox_aplcms_unsupervised" name="RECETOX apLCMS Unsupervised" version="@TOOL_VERSION@+galaxy2"> 1 <tool id="recetox_aplcms_unsupervised" name="RECETOX apLCMS Unsupervised" version="@TOOL_VERSION@+galaxy2">
2 <description>generate a feature table from LC/MS spectra</description> 2 <description>generate a feature table from LC/MS spectra</description>
3 <macros> 3 <macros>
4 <import>recetox_aplcms_macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="creator"/>
7
8 <expand macro="requirements"/>
7 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
8 sh ${symlink_inputs} && 10 sh ${symlink_inputs} &&
9 Rscript -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")' 11 Rscript -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")'
10 ]]></command> 12 ]]></command>
11 <expand macro="creator" />
12 <configfiles> 13 <configfiles>
13 <configfile name="symlink_inputs"> 14 <configfile name="symlink_inputs">
14 #for $infile in $files 15 #for $infile in $files
15 ln -s '${infile}' '${infile.element_identifier}' 16 ln -s '${infile}' '${infile.element_identifier}'
16 #end for 17 #end for
50 ) 51 )
51 ]]></configfile> 52 ]]></configfile>
52 </configfiles> 53 </configfiles>
53 54
54 <expand macro="inputs"> 55 <expand macro="inputs">
55 <expand macro="noise_filtering" /> 56 <expand macro="noise_filtering"/>
56 <expand macro="feature_detection" /> 57 <expand macro="feature_detection"/>
57 <expand macro="peak_alignment" /> 58 <expand macro="peak_alignment"/>
58 <expand macro="weak_signal_recovery" /> 59 <expand macro="weak_signal_recovery"/>
59 <expand macro="output_format" /> 60 <expand macro="output_format"/>
60 </expand> 61 </expand>
61 62
62 <outputs> 63 <outputs>
63 <expand macro="unsupervised_outputs" /> 64 <expand macro="unsupervised_outputs"/>
64 </outputs> 65 </outputs>
65 66
66 <tests> 67 <tests>
67 <test> 68 <test>
68 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" /> 69 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
69 <output name="recovered_feature_sample_table" file="unsupervised_recovered_feature_sample_table.parquet" ftype="parquet"/> 70 <output name="recovered_feature_sample_table" file="unsupervised_recovered_feature_sample_table.parquet"
71 ftype="parquet"/>
70 </test> 72 </test>
71 <test> 73 <test>
72 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" /> 74 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
73 <section name="output_format"> 75 <section name="output_format">
74 <param name="out_format" value="recetox" /> 76 <param name="out_format" value="recetox"/>
75 </section> 77 </section>
76 <output name="recovered_feature_sample_table" file="unsupervised.recetox.parquet" ftype="parquet"/> 78 <output name="recovered_feature_sample_table" file="unsupervised.recetox.parquet" ftype="parquet"/>
77 </test> 79 </test>
78 </tests> 80 </tests>
79 81
80 <help> 82 <help>
81 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or 83 <![CDATA[
82 any historically detected features. For such functionality please use the Hybrid version of apLCMS. 84 @HELP_unsupervised@
83 85 ]]>
84 @GENERAL_HELP@
85 </help> 86 </help>
86 87
87 <expand macro="citations" /> 88 <expand macro="citations"/>
88 </tool> 89 </tool>