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comparison spectral_matching.xml @ 5:bb2b9ede0484 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
author tomnl
date Wed, 04 Apr 2018 16:51:32 -0400
parents 428e5f61850b
children c6d0d9ae8f0b
comparison
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4:428e5f61850b 5:bb2b9ede0484
1 <tool id="spectral_matching" name="spectral_matching" version="0.0.18"> 1 <tool id="spectral_matching" name="spectral_matching" version="0.0.19">
2 <description>
3 Perform spectral matching to spectral libraries using dot product cosine on a MS/MS dataset
4 </description>
5
2 <macros> 6 <macros>
3 <import>macros.xml</import> 7 <import>macros.xml</import>
4 </macros> 8 </macros>
5 9
6 <expand macro="requirements"> 10 <expand macro="requirements">
7 </expand> 11 </expand>
8 12
9 <description> 13
10 Perform spectral matching to spectral libraries using dot product cosine on a MS/MS dataset
11 </description>
12 <stdio> 14 <stdio>
13 <exit_code range="1:" /> 15 <exit_code range="1:" />
14 </stdio> 16 </stdio>
15 <command interpreter="Rscript"><![CDATA[ 17 <command interpreter="Rscript"><![CDATA[
16 spectral_matching.R 18 spectral_matching.R
140 <outputs> 142 <outputs>
141 143
142 144
143 145
144 <data name="sqlite_results" format="sqlite" label="${tool.name} on ${on_string}: SQLite results" 146 <data name="sqlite_results" format="sqlite" label="${tool.name} on ${on_string}: SQLite results"
145 from_work_dir="results.sqlite" visible="true"> 147 from_work_dir="results.sqlite" >
146 <filter>create_new_database is True</filter> 148 <filter>create_new_database is True</filter>
147 </data> 149 </data>
148 <data name="scan_hits" format="tsv" label="${tool.name} on ${on_string}: scan hits" 150 <data name="scan_hits" format="tsv" label="${tool.name} on ${on_string}: scan hits"
149 from_work_dir="scan_hits.tsv" visible="true"/> 151 from_work_dir="scan_hits.tsv" />
150 <data name="xcms_hits" format="tsv" label="${tool.name} on ${on_string}: xcms hits" 152 <data name="xcms_hits" format="tsv" label="${tool.name} on ${on_string}: xcms hits"
151 from_work_dir="xcms_hits.tsv" visible="true"/> 153 from_work_dir="xcms_hits.tsv" />
152 </outputs> 154 </outputs>
153 <tests> 155 <tests>
154 <!--<test>--> 156 <test>
155 157
156 <!--<param name="target_db" value="alldata.sqlite" />--> 158 <param name="target_db" value="alldata.sqlite" />
157 <!--<param name="library_db" value="https://www.dropbox.com/s/csxj6pairsgd8fe/library_spectra.db?dl=0"/>--> 159 <param name="library_db" value="library_spectra.db"/>
158 <!--<output name="xcms_hits" value="spectra_matching_xcms_hits.tsv" />--> 160 <output name="xcms_hits" value="xcms_hits.tsv" />
159 <!--<output name="scan_hits" value="spectra_matching_scan_hits.tsv" />--> 161 <output name="scan_hits" value="scan_hits.tsv" />
160 162
161 <!--</test>--> 163 </test>
162 </tests> 164 </tests>
163 <expand macro="citations" /> 165
166
164 <help><![CDATA[ 167 <help><![CDATA[
165 ============================================================= 168 =============================================================
166 Spectral matching 169 Spectral matching
167 ============================================================= 170 =============================================================
168 ----------- 171 -----------
195 * xcms_hits: All spectral matching hits that can be linked to an XCMS grouped feature 198 * xcms_hits: All spectral matching hits that can be linked to an XCMS grouped feature
196 * sqlite_results (if create_new_db==True): SQLite database of all data including spectral matching results 199 * sqlite_results (if create_new_db==True): SQLite database of all data including spectral matching results
197 200
198 201
199 ]]></help> 202 ]]></help>
203
204 <expand macro="citations"> </expand>
200 </tool> 205 </tool>