Mercurial > repos > lecorguille > xcms_group

comparison abims_xcms_group.xml @ 4:2db1d1d0f131 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
author lecorguille
date Fri, 08 Apr 2016 10:39:09 -0400
parents 98e33cdf0eb1
children 0306a96cc446
comparison
equal deleted inserted replaced
3:98e33cdf0eb1 4:2db1d1d0f131
1 <tool id="abims_xcms_group" name="xcms.group" version="2.0.4"> 1 <tool id="abims_xcms_group" name="xcms.group" version="2.0.5">
2 2
3 <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description> 3 <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>
4 4
5 <requirements> 5 <macros>
6 <requirement type="package" version="3.1.2">R</requirement> 6 <import>macros.xml</import>
7 <requirement type="binary">Rscript</requirement> 7 </macros>
8 <requirement type="package" version="1.44.0">xcms</requirement> 8
9 <requirement type="package" version="2.2.0">xcms_w4m_script</requirement> 9 <expand macro="requirements"/>
10 </requirements> 10 <expand macro="stdio"/>
11
12 <stdio>
13 <exit_code range="1:" level="fatal" />
14 </stdio>
15 11
16 <command><![CDATA[ 12 <command><![CDATA[
17 xcms.r 13 @COMMAND_XCMS_SCRIPT@
18 xfunction group 14 xfunction group
19 image $image 15 image $image
20 16
21 xsetRdataOutput $xsetRData 17 xsetRdataOutput $xsetRData
22 rplotspdf $rplotsPdf 18 rplotspdf $rplotsPdf
39 mzVsRTbalance $methods.mzVsRTbalance 35 mzVsRTbalance $methods.mzVsRTbalance
40 mzCheck $methods.mzCheck 36 mzCheck $methods.mzCheck
41 rtCheck $methods.rtCheck 37 rtCheck $methods.rtCheck
42 kNN $methods.kNN 38 kNN $methods.kNN
43 #end if 39 #end if
44 ; 40 @COMMAND_LOG_EXIT@
45 return=\$?;
46 mv log.txt $log;
47 cat $log;
48 sh -c "exit \$return"
49
50 ]]></command> 41 ]]></command>
51 42
52 <inputs> 43 <inputs>
53 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> 44 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
54 <conditional name="methods"> 45 <conditional name="methods">
107 </outputs> 98 </outputs>
108 99
109 <tests> 100 <tests>
110 <test> 101 <test>
111 <param name="image" value="xset.RData"/> 102 <param name="image" value="xset.RData"/>
112 <param name="methods.method" value="density"/> 103 <param name="methods|method" value="density"/>
113 <param name="methods.bw" value="5"/> 104 <param name="methods|bw" value="5"/>
114 <param name="methods.minfrac" value="0.3"/> 105 <param name="methods|minfrac" value="0.3"/>
115 <param name="methods.mzwid" value="0.01"/> 106 <param name="methods|mzwid" value="0.01"/>
116 <param name="methods.density_options.option" value="show"/> 107 <param name="methods|density_options|option" value="show"/>
117 <param name="methods.density_options.max" value="50"/> 108 <param name="methods|density_options|max" value="50"/>
118 <!--<output name="xsetRData" file="xset.group.RData" />-->
119 <!--<output name="rplotsPdf" file="xset.group.Rplots.pdf" />-->
120 <output name="log"> 109 <output name="log">
121 <assert_contents> 110 <assert_contents>
122 <has_text text="object with 9 samples" /> 111 <has_text text="object with 4 samples" />
123 <has_text text="Time range: 0.7-1140 seconds (0-19 minutes)" /> 112 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
124 <has_text text="Mass range: 50.0019-999.9863 m/z" /> 113 <has_text text="Mass range: 50.0021-999.9863 m/z" />
125 <has_text text="Peaks: 135846 (about 15094 per sample)" /> 114 <has_text text="Peaks: 59359 (about 14840 per sample)" />
126 <has_text text="Peak Groups: 6642" /> 115 <has_text text="Peak Groups: 48998" />
127 <has_text text="Sample classes: bio, blank" /> 116 <has_text text="Sample classes: bio, blank" />
128 </assert_contents> 117 </assert_contents>
129 </output> 118 </output>
130 119 </test>
120 <test>
121 <param name="image" value="xset.group.retcor.RData"/>
122 <param name="methods|method" value="density"/>
123 <param name="methods|bw" value="5"/>
124 <param name="methods|minfrac" value="0.3"/>
125 <param name="methods|mzwid" value="0.01"/>
126 <param name="methods|density_options|option" value="show"/>
127 <param name="methods|density_options|max" value="50"/>
128 <output name="log">
129 <assert_contents>
130 <has_text text="object with 4 samples" />
131 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
132 <has_text text="Mass range: 50.0021-999.9863 m/z" />
133 <has_text text="Peaks: 59359 (about 14840 per sample)" />
134 <has_text text="Peak Groups: 48958" />
135 <has_text text="Sample classes: bio, blank" />
136 </assert_contents>
137 </output>
131 </test> 138 </test>
132 </tests> 139 </tests>
133 140
134 <help><![CDATA[ 141 <help><![CDATA[
135 142
136 .. class:: infomark 143 @HELP_AUTHORS@
137
138 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
139
140 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]
141
142 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
143
144
145
146 ---------------------------------------------------
147 144
148 ========== 145 ==========
149 Xcms.Group 146 Xcms.Group
150 ========== 147 ==========
151 148
275 --------------------------------------------------- 272 ---------------------------------------------------
276 273
277 Changelog/News 274 Changelog/News
278 -------------- 275 --------------
279 276
277 **Version 2.0.5 - 04/04/2016**
278
279 - TEST: refactoring to pass planemo test using conda dependencies
280
281
280 **Version 2.0.4 - 10/02/2016** 282 **Version 2.0.4 - 10/02/2016**
281 283
282 - BUGFIX: better management of errors. Datasets remained green although the process failed 284 - BUGFIX: better management of errors. Datasets remained green although the process failed
283 285
284 - UPDATE: refactoring of internal management of inputs/outputs 286 - UPDATE: refactoring of internal management of inputs/outputs
294 296
295 297
296 ]]></help> 298 ]]></help>
297 299
298 300
299 <citations> 301 <expand macro="citation" />
300 <citation type="doi">10.1021/ac051437y</citation>
301 <citation type="doi">10.1093/bioinformatics/btu813</citation>
302 </citations>
303 302
304 303
305 </tool> 304 </tool>