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comparison ramclustr.xml @ 0:cb0b83b330fd draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
author recetox
date Wed, 28 Jul 2021 08:42:02 +0000
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children 15e173c5762c
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-1:000000000000 0:cb0b83b330fd
1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy1">
2 <macros>
3 <import>ramclustr_macros.xml</import>
4 </macros>
5
6 <requirements>
7 <container type="docker">recetox/ramclustr:1.1.0-recetox0</container>
8 </requirements>
9
10 <command detect_errors="aggressive"><![CDATA[
11 Rscript
12 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
13 #if $filetype.type_choice == "xcms":
14 -e 'x <- ramclustr_xcms(
15 input_xcms = "$filetype.input_xcms",
16 #else:
17 -e 'x <- ramclustr_csv(
18 ms="$filetype.ms_csv.ms",
19 idmsms="$filetype.ms_csv.idmsms",
20 feature_delimiter="$filetype.ms_csv.feature_delimiter",
21 sample_name_column = $filetype.ms_csv.sample_name_column,
22 retention_time_column= $filetype.ms_csv.retention_time_column,
23 #end if
24 sr = $filetype.required.sr,
25 deep_split = $filetype.required.deepSplit,
26 block_size = $filetype.required.blocksize,
27 mult = $filetype.required.mult,
28 hmax = $filetype.required.hmax,
29 collapse = $filetype.required.collapse,
30 use_pheno = $filetype.required.usePheno,
31 qc_inj_range = $filetype.required.qc_inj_range,
32 normalize = "$filetype.required.normalize",
33 min_module_size = $filetype.required.minModuleSize,
34 linkage = "$filetype.required.linkage",
35 mzdec = $filetype.required.mzdec,
36 cor_method = "$filetype.required.cor_method",
37 rt_only_low_n = $filetype.required.rt_only_low_n,
38 replace_zeros = $filetype.required.replace_zeros,
39 #if $filetype.type_choice == "xcms":
40 #if $filetype.optional.st
41 st = $filetype.optional.st,
42 #end if
43 #else:
44 st = $filetype.ms_csv.st,
45 #end if
46 #if $filetype.optional.maxt
47 maxt = $filetype.optional.maxt,
48 #end if
49 #if $filetype.optional.fftempdir
50 fftempdir = $filetype.optional.fftempdir,
51 #end if
52 #if $filetype.metadata.batch_order_qc
53 metadata_file = "${filetype.metadata.batch_order_qc}",
54 #end if
55 )'
56 -e 'store_output(x, "$result", "$method_metadata", $filetype.required.merge_msp, "$spec_abundance")'
57 ]]>
58 </command>
59
60 <inputs>
61 <conditional name="filetype">
62 <param name="type_choice" type="select" label="Choose input format:">
63 <option value="xcms" selected="true">XCMS</option>
64 <option value="csv">CSV</option>
65 </param>
66 <when value="xcms">
67 <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help=": containing grouped feature data for clustering by ramclustR" />
68 <expand macro="parameters_required" />
69 <expand macro="parameters_optional_xcms" />
70 <expand macro="parameters_optional_metadata" />
71 </when>
72 <when value="csv">
73 <expand macro="parameters_csv" />
74 <expand macro="parameters_required" />
75 <expand macro="parameters_optional_csv" />
76 <expand macro="parameters_optional_metadata" />
77 </when>
78 </conditional>
79 </inputs>
80
81 <outputs>
82 <data label="${tool.name} on ${on_string}" name="result" format="RData" />
83 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
84 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
85 <expand macro="output_msp"/>
86 </outputs>
87
88 <tests>
89 <test>
90 <param name="type_choice" value="xcms"/>
91 <param name="input_xcms" value="xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
92 <output name="result" file="ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="100"/>
93 <output_collection name="mass_spectra" type="list">
94 <element name="fill" file="fill_xcms_1.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/>
95 </output_collection>
96 <output name="method_metadata" file="metadata_xcms_1.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/>
97 <output name="spec_abundance" file="spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
98 </test>
99 <test>
100 <param name="type_choice" value="xcms"/>
101 <param name="input_xcms" value="xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
102 <param name="batch_order_qc" value="sample_metadata_xcms_2.csv" ftype="csv" />
103 <output name="result" file="ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
104 <output_collection name="mass_spectra" type="list">
105 <element name="fill" file="fill_xcms_2.msp" ftype="msp" lines_diff="10"/>
106 </output_collection>
107 <output name="method_metadata" file="metadata_xcms_2.txt" ftype="txt" checksum="md5$286e4aa53c38c99e92202584d7407406"/>
108 <output name="spec_abundance" file="spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
109 </test>
110 <test>
111 <param name="type_choice" value="csv"/>
112 <param name="ms" value="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"/>
117 <param name="sr" value="0.5"/>
118 <param name="deepSplit" value="False"/>
119 <param name="blocksize" value="1000"/>
120 <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"/>
134 <output name="result" file="ramclustObj_csv_1.rdata"/>
135 <output name="spec_abundance" file="spec_abundance_csv_1.csv" ftype="csv"/>
136 <output name="method_metadata" file="metadata_csv_1.txt" ftype="txt"/>
137 <output_collection name="mass_spectra" type="list">
138 <element name="fill" file="spectra_csv_1.msp" ftype="msp"/>
139 </output_collection>
140 </test>
141 <test>
142 <param name="type_choice" value="csv"/>
143 <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
144 <param name="sample_name_column" value="1"/>
145 <param name="feature_delimiter" value="_"/>
146 <param name="retention_time_column" value="2"/>
147 <param name="batch_order_qc" value="sample_metadata_csv_2.csv" ftype="csv" />
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">
152 <element name="fill" file="spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
153 </output_collection>
154 </test>
155 </tests>
156
157 <help>
158 Documentation
159 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
160
161 Upstream Tools
162 +-------+----------------------+----------------------+------------+
163 | Name | Output File | Format | Parameter |
164 +=======+======================+======================+============+
165 | xcms | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj |
166 +-------+----------------------+----------------------+------------+
167
168 The tool takes an **xcmsSet** object as input and extracts all relevant information.
169
170 +-------+------------------------+--------+------------+
171 | Name | Output File | Format | Parameter |
172 +=======+========================+========+============+
173 | ??? | Feature Table with MS1 | csv | ms |
174 +-------+------------------------+--------+------------+
175 | ??? | Feature Table with MS2 | csv | idmsms |
176 +-------+------------------------+--------+------------+
177
178 Alternatively, the tool takes a **csv** table as input which has to fulfill the following requirements
179
180 (1) no more than one sample (or file) name column and one feature name row;
181 (2) feature names that contain the mass and retention times, separated by a constant delimiter; and
182 (3) features in columns and samples in rows.
183
184 Downstream Tools
185 +---------+--------------+----------------------+
186 | Name | Output File | Format |
187 +=========+==============+======================+
188 | matchMS | Mass Spectra | collection (tgz/msp) |
189 +---------+--------------+----------------------+
190
191 @GENERAL_HELP@
192 </help>
193
194 <expand macro="citations" />
195 </tool>