Mercurial > repos > recetox > ramclustr

comparison ramclustr.xml @ 3:211cd88b5148 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 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:25:33 +0000
parents eac0e6feb850
children 69e0da4703b5
comparison
equal deleted inserted replaced
2:eac0e6feb850 3:211cd88b5148
1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy0">
2 <macros> 2 <macros>
3 <import>ramclustr_macros.xml</import> 3 <import>macros.xml</import>
4 </macros> 4 </macros>
5 <creator> 5 <expand macro="creator"/>
6 <organization 6
7 url="https://www.recetox.muni.cz/"
8 name="RECETOX MUNI" />
9 </creator>
10 <requirements> 7 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
12 <requirement type="package" version="3.14.0">bioconductor-xcms</requirement> 9 <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>
13 </requirements> 10 </requirements>
11
14 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
15 Rscript 13 Rscript
16 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")' 14 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
17 -e 'source("${ramclustr_method}")' 15 -e 'source("${ramclustr_method}")'
18 ]]> 16 ]]>
71 <param name="type_choice" type="select" label="Choose input format:"> 69 <param name="type_choice" type="select" label="Choose input format:">
72 <option value="xcms" selected="true">XCMS</option> 70 <option value="xcms" selected="true">XCMS</option>
73 <option value="csv">CSV</option> 71 <option value="csv">CSV</option>
74 </param> 72 </param>
75 <when value="xcms"> 73 <when value="xcms">
76 <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help=": containing grouped feature data for clustering by ramclustR" /> 74 <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help="Grouped feature data for clustering by ramclustR" />
77 <expand macro="parameters_required" /> 75 <expand macro="parameters_required" />
78 <expand macro="parameters_optional_xcms" /> 76 <expand macro="parameters_optional_xcms" />
79 <expand macro="parameters_optional_metadata" /> 77 <expand macro="parameters_optional_metadata" />
80 </when> 78 </when>
81 <when value="csv"> 79 <when value="csv">
142 </output_collection> 140 </output_collection>
143 </test> 141 </test>
144 </tests> 142 </tests>
145 143
146 <help> 144 <help>
147 Documentation 145 <![CDATA[
148 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd 146 @HELP@
149 147 ]]>
150 Upstream Tools
151 +-------+----------------------+----------------------+------------+
152 | Name | Output File | Format | Parameter |
153 +=======+======================+======================+============+
154 | xcms | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj |
155 +-------+----------------------+----------------------+------------+
156
157 The tool takes an **xcmsSet** object as input and extracts all relevant information.
158
159 +-------+------------------------+--------+------------+
160 | Name | Output File | Format | Parameter |
161 +=======+========================+========+============+
162 | ??? | Feature Table with MS1 | csv | ms |
163 +-------+------------------------+--------+------------+
164 | ??? | Feature Table with MS2 | csv | idmsms |
165 +-------+------------------------+--------+------------+
166
167 Alternatively, the tool takes a **csv** table as input which has to fulfill the following requirements
168
169 (1) no more than one sample (or file) name column and one feature name row;
170 (2) feature names that contain the mass and retention times, separated by a constant delimiter; and
171 (3) features in columns and samples in rows.
172
173 Downstream Tools
174 +---------+--------------+----------------------+
175 | Name | Output File | Format |
176 +=========+==============+======================+
177 | matchMS | Mass Spectra | collection (tgz/msp) |
178 +---------+--------------+----------------------+
179
180 @GENERAL_HELP@
181 </help> 148 </help>
182 149
183 <expand macro="citations" /> 150 <expand macro="citations" />
184 </tool> 151 </tool>