Mercurial > repos > lecorguille > xcms_group

comparison abims_xcms_group.xml @ 3:98e33cdf0eb1 draft

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planemo upload
author lecorguille
date Mon, 22 Feb 2016 16:31:48 -0500
parents ed149026836e
children 2db1d1d0f131
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2:ed149026836e 3:98e33cdf0eb1
1 <tool id="abims_xcms_group" name="xcms.group" version="2.0.2"> 1 <tool id="abims_xcms_group" name="xcms.group" version="2.0.4">
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 <requirements>
6 <requirement type="package" version="3.1.2">R</requirement> 6 <requirement type="package" version="3.1.2">R</requirement>
7 <requirement type="binary">Rscript</requirement> 7 <requirement type="binary">Rscript</requirement>
8 <requirement type="package" version="1.44.0">xcms</requirement> 8 <requirement type="package" version="1.44.0">xcms</requirement>
9 <requirement type="package" version="2.1">xcms_w4m_script</requirement> 9 <requirement type="package" version="2.2.0">xcms_w4m_script</requirement>
10 </requirements> 10 </requirements>
11 11
12 <stdio> 12 <stdio>
13 <exit_code range="1:" level="fatal" /> 13 <exit_code range="1:" level="fatal" />
14 </stdio> 14 </stdio>
15 15
16 <command> 16 <command><![CDATA[
17 xcms.r 17 xcms.r
18 xfunction group image $image method $methods.method sleep 0.001 18 xfunction group
19 image $image
20
21 xsetRdataOutput $xsetRData
22 rplotspdf $rplotsPdf
23
24 method $methods.method sleep 0.001
19 #if $methods.method == "density": 25 #if $methods.method == "density":
20 ## minsamp $methods.minsamp 26 ## minsamp $methods.minsamp
21 minfrac $methods.minfrac 27 minfrac $methods.minfrac
22 bw $methods.bw 28 bw $methods.bw
23 mzwid $methods.mzwid 29 mzwid $methods.mzwid
33 mzVsRTbalance $methods.mzVsRTbalance 39 mzVsRTbalance $methods.mzVsRTbalance
34 mzCheck $methods.mzCheck 40 mzCheck $methods.mzCheck
35 rtCheck $methods.rtCheck 41 rtCheck $methods.rtCheck
36 kNN $methods.kNN 42 kNN $methods.kNN
37 #end if 43 #end if
38 &amp;&amp; ( 44 ;
39 mv group.RData $xsetRData; 45 return=\$?;
40 mv Rplots.pdf $rplotsPdf 46 mv log.txt $log;
41 ); 47 cat $log;
42 cat xset.log 48 sh -c "exit \$return"
43 </command> 49
50 ]]></command>
44 51
45 <inputs> 52 <inputs>
46 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> 53 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
47 <conditional name="methods"> 54 <conditional name="methods">
48 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below"> 55 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below">
94 </inputs> 101 </inputs>
95 102
96 <outputs> 103 <outputs>
97 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/> 104 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
98 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/> 105 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
106 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
99 </outputs> 107 </outputs>
100 108
101 <tests> 109 <tests>
102 <test> 110 <test>
103 <param name="image" value="xset.RData"/> 111 <param name="image" value="xset.RData"/>
105 <param name="methods.bw" value="5"/> 113 <param name="methods.bw" value="5"/>
106 <param name="methods.minfrac" value="0.3"/> 114 <param name="methods.minfrac" value="0.3"/>
107 <param name="methods.mzwid" value="0.01"/> 115 <param name="methods.mzwid" value="0.01"/>
108 <param name="methods.density_options.option" value="show"/> 116 <param name="methods.density_options.option" value="show"/>
109 <param name="methods.density_options.max" value="50"/> 117 <param name="methods.density_options.max" value="50"/>
110 <output name="xsetRData" file="xset.group.RData" /> 118 <!--<output name="xsetRData" file="xset.group.RData" />-->
111 <output name="rplotsPdf" file="xset.group.Rplots.pdf" /> 119 <!--<output name="rplotsPdf" file="xset.group.Rplots.pdf" />-->
120 <output name="log">
121 <assert_contents>
122 <has_text text="object with 9 samples" />
123 <has_text text="Time range: 0.7-1140 seconds (0-19 minutes)" />
124 <has_text text="Mass range: 50.0019-999.9863 m/z" />
125 <has_text text="Peaks: 135846 (about 15094 per sample)" />
126 <has_text text="Peak Groups: 6642" />
127 <has_text text="Sample classes: bio, blank" />
128 </assert_contents>
129 </output>
112 130
113 </test> 131 </test>
114 </tests> 132 </tests>
115 133
116 <help> 134 <help><![CDATA[
117 135
118 .. class:: infomark 136 .. class:: infomark
119 137
120 **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 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
121 139
252 270
253 .. image:: xcms_group.png 271 .. image:: xcms_group.png
254 :width: 700 272 :width: 700
255 273
256 274
257 275 ---------------------------------------------------
258 </help> 276
277 Changelog/News
278 --------------
279
280 **Version 2.0.4 - 10/02/2016**
281
282 - BUGFIX: better management of errors. Datasets remained green although the process failed
283
284 - UPDATE: refactoring of internal management of inputs/outputs
285
286 - UPDATE: refactoring to feed the new report tool
287
288
289 **Version 2.0.2 - 02/06/2015**
290
291 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
292
293 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
294
295
296 ]]></help>
259 297
260 298
261 <citations> 299 <citations>
262 <citation type="doi">10.1021/ac051437y</citation> 300 <citation type="doi">10.1021/ac051437y</citation>
263 <citation type="doi">10.1093/bioinformatics/btu813</citation> 301 <citation type="doi">10.1093/bioinformatics/btu813</citation>