Mercurial > repos > recetox > ramclustr_csv

comparison ramclustr_csv.xml @ 3:61035548f46c draft default tip

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
author recetox
date Mon, 07 Jun 2021 15:13:41 +0000
parents 08b09930cd73
children
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2:08b09930cd73 3:61035548f46c
1 <tool id="ramclustr_csv" name="RAMClustR (CSV)" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="ramclustr_csv" name="RAMClustR (CSV)" version="@TOOL_VERSION@+galaxy1">
2 <macros> 2 <macros>
3 <import>ramclustr_macros.xml</import> 3 <import>ramclustr_macros.xml</import>
4 </macros> 4 </macros>
5 5
6 <requirements> 6 <requirements>
9 9
10 <inputs> 10 <inputs>
11 <expand macro="parameters_csv" /> 11 <expand macro="parameters_csv" />
12 <expand macro="parameters_required" /> 12 <expand macro="parameters_required" />
13 <expand macro="parameters_optional_csv" /> 13 <expand macro="parameters_optional_csv" />
14 <expand macro="parameters_optional_metadata" />
14 </inputs> 15 </inputs>
15 16
16 <command detect_errors="aggressive"><![CDATA[ 17 <command detect_errors="aggressive"><![CDATA[
17 Rscript 18 Rscript
18 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")' 19 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
42 maxt = $optional.maxt, 43 maxt = $optional.maxt,
43 #end if 44 #end if
44 #if $optional.fftempdir 45 #if $optional.fftempdir
45 fftempdir = $optional.fftempdir, 46 fftempdir = $optional.fftempdir,
46 #end if 47 #end if
48 #if $metadata.batch_order_qc
49 metadata = "$metadata.batch_order_qc"
50 #end if
47 )' 51 )'
48 -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")' 52 -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")'
49 53
50 ]]> 54 ]]>
51 </command> 55 </command>
57 <expand macro="output_msp"/> 61 <expand macro="output_msp"/>
58 </outputs> 62 </outputs>
59 63
60 <tests> 64 <tests>
61 <test> 65 <test>
62 <param name="ms" value="csv_test-input.csv" ftype="csv"/> 66 <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
63 <param name="sample_name_column" value="1"/> 67 <param name="sample_name_column" value="1"/>
64 <param name="feature_delimiter" value="_"/> 68 <param name="feature_delimiter" value="_"/>
65 <param name="retention_time_column" value="2"/> 69 <param name="retention_time_column" value="2"/>
66 <param name="st" value="5.0"/> 70 <param name="st" value="5.0"/>
67 <param name="sr" value="0.5"/> 71 <param name="sr" value="0.5"/>
79 <param name="cor_method" value="pearson"/> 83 <param name="cor_method" value="pearson"/>
80 <param name="rt_only_low_n" value="True"/> 84 <param name="rt_only_low_n" value="True"/>
81 <param name="replace_zeros" value="True"/> 85 <param name="replace_zeros" value="True"/>
82 <param name="Merge MSP Files" value="True"/> 86 <param name="Merge MSP Files" value="True"/>
83 <param name="maxt" value="1"/> 87 <param name="maxt" value="1"/>
84 <output name="result" file="ramclustR-csv_object.RData"/> 88 <output name="result" file="ramclustObj_csv_1.rdata"/>
85 <output name="spec_abundance" file="spec-abundance_csv.csv" ftype="csv"/> 89 <output name="spec_abundance" file="spec_abundance_csv_1.csv" ftype="csv"/>
86 <output name="method_metadata" file="metadata_csv.txt" ftype="txt"/> 90 <output name="method_metadata" file="metadata_csv_1.txt" ftype="txt"/>
87 <output_collection name="mass_spectra" type="list"> 91 <output_collection name="mass_spectra" type="list">
88 <element name="fill" file="test-spectra_csv.msp" ftype="msp"/> 92 <element name="fill" file="spectra_csv_1.msp" ftype="msp"/>
93 </output_collection>
94 </test>
95 <test>
96 <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
97 <param name="sample_name_column" value="1"/>
98 <param name="feature_delimiter" value="_"/>
99 <param name="retention_time_column" value="2"/>
100 <param name="batch_order_qc" value="sample_metadata_csv_2.csv" ftype="csv" />
101 <output name="result" file="ramclustObj_csv_2.rdata"/>
102 <output name="spec_abundance" file="spec_abundance_csv_2.csv" ftype="csv"/>
103 <output name="method_metadata" file="metadata_csv_2.txt" ftype="txt"/>
104 <output_collection name="mass_spectra" type="list">
105 <element name="fill" file="spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
89 </output_collection> 106 </output_collection>
90 </test> 107 </test>
91 </tests> 108 </tests>
92 109
93 <help> 110 <help>