Mercurial > repos > recetox > ramclustr

comparison ramclustr.xml @ 1:15e173c5762c draft

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/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
author recetox
date Thu, 19 Aug 2021 07:17:15 +0000
parents cb0b83b330fd
children eac0e6feb850
comparison
equal deleted inserted replaced
0:cb0b83b330fd 1:15e173c5762c
1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy0">
2 <macros> 2 <macros>
3 <import>ramclustr_macros.xml</import> 3 <import>ramclustr_macros.xml</import>
4 </macros> 4 </macros>
5 5 <creator>
6 <organization
7 url="https://www.recetox.muni.cz/"
8 name="RECETOX MUNI" />
9 </creator>
6 <requirements> 10 <requirements>
7 <container type="docker">recetox/ramclustr:1.1.0-recetox0</container> 11 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
12 <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>
8 </requirements> 13 </requirements>
9
10 <command detect_errors="aggressive"><![CDATA[ 14 <command detect_errors="aggressive"><![CDATA[
11 Rscript 15 Rscript
12 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")' 16 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
13 #if $filetype.type_choice == "xcms": 17 #if $filetype.type_choice == "xcms":
14 -e 'x <- ramclustr_xcms( 18 -e 'x <- ramclustr_xcms(
54 #end if 58 #end if
55 )' 59 )'
56 -e 'store_output(x, "$result", "$method_metadata", $filetype.required.merge_msp, "$spec_abundance")' 60 -e 'store_output(x, "$result", "$method_metadata", $filetype.required.merge_msp, "$spec_abundance")'
57 ]]> 61 ]]>
58 </command> 62 </command>
59
60 <inputs> 63 <inputs>
61 <conditional name="filetype"> 64 <conditional name="filetype">
62 <param name="type_choice" type="select" label="Choose input format:"> 65 <param name="type_choice" type="select" label="Choose input format:">
63 <option value="xcms" selected="true">XCMS</option> 66 <option value="xcms" selected="true">XCMS</option>
64 <option value="csv">CSV</option> 67 <option value="csv">CSV</option>
84 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/> 87 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
85 <expand macro="output_msp"/> 88 <expand macro="output_msp"/>
86 </outputs> 89 </outputs>
87 90
88 <tests> 91 <tests>
89 <test> 92 <test><!-- TEST 1 -->
90 <param name="type_choice" value="xcms"/> 93 <param name="type_choice" value="xcms"/>
91 <param name="input_xcms" value="xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/> 94 <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
92 <output name="result" file="ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="100"/> 95 <output name="result" file="test1_ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="200"/>
93 <output_collection name="mass_spectra" type="list"> 96 <output_collection name="mass_spectra" type="list">
94 <element name="fill" file="fill_xcms_1.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/> 97 <element name="fill" file="test1_fill_xcms_1.msp" ftype="msp"/>
95 </output_collection> 98 </output_collection>
96 <output name="method_metadata" file="metadata_xcms_1.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/> 99 <output name="method_metadata" file="test1_metadata_xcms_1.txt" ftype="txt"/>
97 <output name="spec_abundance" file="spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/> 100 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
98 </test> 101 </test>
99 <test> 102 <test><!-- TEST 2 -->
100 <param name="type_choice" value="xcms"/> 103 <param name="type_choice" value="xcms"/>
101 <param name="input_xcms" value="xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/> 104 <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
102 <param name="batch_order_qc" value="sample_metadata_xcms_2.csv" ftype="csv" /> 105 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
103 <output name="result" file="ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/> 106 <output name="result" file="test2_ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
104 <output_collection name="mass_spectra" type="list"> 107 <output_collection name="mass_spectra" type="list">
105 <element name="fill" file="fill_xcms_2.msp" ftype="msp" lines_diff="10"/> 108 <element name="fill" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="10"/>
106 </output_collection> 109 </output_collection>
107 <output name="method_metadata" file="metadata_xcms_2.txt" ftype="txt" checksum="md5$286e4aa53c38c99e92202584d7407406"/> 110 <output name="method_metadata" file="test2_metadata_xcms_2.txt" ftype="txt"/>
108 <output name="spec_abundance" file="spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/> 111 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
109 </test> 112 </test>
110 <test> 113 <test><!-- TEST 3 -->
111 <param name="type_choice" value="csv"/> 114 <param name="type_choice" value="csv"/>
112 <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/> 115 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
113 <param name="sample_name_column" value="1"/>
114 <param name="feature_delimiter" value="_"/>
115 <param name="retention_time_column" value="2"/>
116 <param name="st" value="5.0"/> 116 <param name="st" value="5.0"/>
117 <param name="sr" value="0.5"/>
118 <param name="deepSplit" value="False"/>
119 <param name="blocksize" value="1000"/> 117 <param name="blocksize" value="1000"/>
120 <param name="mult" value="1"/> 118 <param name="mult" value="1"/>
121 <param name="hmax" value="0.3"/>
122 <param name="collapse" value="True"/>
123 <param name="usePheno" value="True"/>
124 <param name="normalize" value="none"/>
125 <param name="qc_inj_range" value="20"/>
126 <param name="minModuleSize" value="2"/>
127 <param name="linkage" value="average"/>
128 <param name="mzdec" value="3"/>
129 <param name="cor_method" value="pearson"/>
130 <param name="rt_only_low_n" value="True"/>
131 <param name="replace_zeros" value="True"/>
132 <param name="Merge MSP Files" value="True"/>
133 <param name="maxt" value="1"/> 119 <param name="maxt" value="1"/>
134 <output name="result" file="ramclustObj_csv_1.rdata"/> 120 <output name="result" file="test3_ramclustObj_csv_1.rdata" ftype="RData" compare="sim_size" delta="200"/>
135 <output name="spec_abundance" file="spec_abundance_csv_1.csv" ftype="csv"/> 121 <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/>
136 <output name="method_metadata" file="metadata_csv_1.txt" ftype="txt"/> 122 <output name="method_metadata" file="test3_metadata_csv_1.txt" ftype="txt"/>
137 <output_collection name="mass_spectra" type="list"> 123 <output_collection name="mass_spectra" type="list">
138 <element name="fill" file="spectra_csv_1.msp" ftype="msp"/> 124 <element name="fill" file="test3_spectra_csv_1.msp" ftype="msp"/>
139 </output_collection> 125 </output_collection>
140 </test> 126 </test>
141 <test> 127 <test><!-- TEST 4 -->
142 <param name="type_choice" value="csv"/> 128 <param name="type_choice" value="csv"/>
143 <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/> 129 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
144 <param name="sample_name_column" value="1"/> 130 <param name="batch_order_qc" value="test4_sample_metadata_csv_2.csv" ftype="csv" />
145 <param name="feature_delimiter" value="_"/> 131 <output name="result" file="test4_ramclustObj_csv_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
146 <param name="retention_time_column" value="2"/> 132 <output name="spec_abundance" file="test4_spec_abundance_csv_2.csv" ftype="csv"/>
147 <param name="batch_order_qc" value="sample_metadata_csv_2.csv" ftype="csv" /> 133 <output name="method_metadata" file="test4_metadata_csv_2.txt" ftype="txt"/>
148 <output name="result" file="ramclustObj_csv_2.rdata"/>
149 <output name="spec_abundance" file="spec_abundance_csv_2.csv" ftype="csv"/>
150 <output name="method_metadata" file="metadata_csv_2.txt" ftype="txt"/>
151 <output_collection name="mass_spectra" type="list"> 134 <output_collection name="mass_spectra" type="list">
152 <element name="fill" file="spectra_csv_2.msp" ftype="msp" lines_diff="10"/> 135 <element name="fill" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
153 </output_collection> 136 </output_collection>
154 </test> 137 </test>
155 </tests> 138 </tests>
156 139
157 <help> 140 <help>