Mercurial > repos > lecorguille > xcms_retcor

comparison abims_xcms_retcor.xml @ 2:54cc3edfe35c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
author lecorguille
date Fri, 08 Apr 2016 10:39:32 -0400
parents da716e2937f2
children 3b44991a8e05
comparison
equal deleted inserted replaced
1:da716e2937f2 2:54cc3edfe35c
1 <tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.5"> 1 <tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.6">
2 2
3 <description>Retention Time Correction using retcor function from xcms R package </description> 3 <description>Retention Time Correction using retcor function from xcms R package </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 image $image 14 image $image
19 xfunction retcor 15 xfunction retcor
20 16
21 xsetRdataOutput $xsetRData 17 xsetRdataOutput $xsetRData
22 ticspdf $ticsCorPdf 18 ticspdf $ticsCorPdf
34 span $methods.options.span 30 span $methods.options.span
35 family $methods.options.family 31 family $methods.options.family
36 plottype $methods.options.plottype 32 plottype $methods.options.plottype
37 #end if 33 #end if
38 #end if 34 #end if
39 ###if $zip_file: 35 #if $zip_file:
40 ## zipfile $zip_file 36 zipfile $zip_file
41 ###end if 37 #end if
42 ; 38 @COMMAND_LOG_EXIT@
43 return=\$?;
44 mv log.txt $log;
45 cat $log;
46 sh -c "exit \$return"
47
48 ]]></command> 39 ]]></command>
49 40
50 <inputs> 41 <inputs>
51 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> 42 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
52 <conditional name="methods"> 43 <conditional name="methods">
62 <option value="loess">loess</option> 53 <option value="loess">loess</option>
63 <option value="linear">linear</option> 54 <option value="linear">linear</option>
64 </param> 55 </param>
65 <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" /> 56 <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" />
66 <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" /> 57 <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" />
58
67 <conditional name="options"> 59 <conditional name="options">
68 <param name="option" type="select" label="Advanced options"> 60 <param name="option" type="select" label="Advanced options">
69 <option value="show">show</option> 61 <option value="show">show</option>
70 <option value="hide" selected="true">hide</option> 62 <option value="hide" selected="true">hide</option>
71 </param> 63 </param>
80 <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> 72 <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density">
81 <option value="none" selected="true">none</option> 73 <option value="none" selected="true">none</option>
82 <option value="deviation">deviation</option> 74 <option value="deviation">deviation</option>
83 <option value="mdevden">mdevden</option> 75 <option value="mdevden">mdevden</option>
84 </param> 76 </param>
77
85 </when> 78 </when>
86 <when value="hide"> 79 <when value="hide">
87 </when> 80 </when>
88 </conditional> 81 </conditional>
89 </when> 82 </when>
90 </conditional> 83 </conditional>
91 <!-- To pass planemo test --> 84 <!-- To pass planemo test -->
92 <!--<param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" />--> 85 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." />
93 </inputs> 86 </inputs>
94 87
95 <outputs> 88 <outputs>
96 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" /> 89 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" />
97 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.retcor.Rplots.pdf"> 90 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.retcor.Rplots.pdf">
106 </outputs> 99 </outputs>
107 100
108 <tests> 101 <tests>
109 <test> 102 <test>
110 <param name="image" value="xset.group.RData"/> 103 <param name="image" value="xset.group.RData"/>
111 <param name="methods.method" value="peakgroups"/> 104 <param name="methods|method" value="peakgroups"/>
112 <param name="methods.smooth" value="loess"/> 105 <param name="methods|smooth" value="loess"/>
113 <param name="methods.extra" value="1"/> 106 <param name="methods|extra" value="1"/>
114 <param name="methods.missing" value="1"/> 107 <param name="methods|missing" value="1"/>
115 <param name="methods.options.option" value="show"/> 108 <param name="methods|options|option" value="show"/>
116 <param name="methods.options.span" value="0.2"/> 109 <param name="methods|options|span" value="0.2"/>
117 <param name="methods.options.family" value="gaussian"/> 110 <param name="methods|options|family" value="gaussian"/>
118 <param name="methods.options.plottype" value="deviation"/> 111 <param name="methods|options|plottype" value="deviation"/>
119 <param name="zip_file" value="sacuri.zip"/> 112 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" />
120 <!--<output name="xsetRData" file="xset.group.retcor.RData" />-->
121 <!--<output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" />-->
122 <!--<output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" />-->
123 <!--<output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.pdf" />-->
124 <output name="log"> 113 <output name="log">
125 <assert_contents> 114 <assert_contents>
126 <has_text text="object with 9 samples" /> 115 <has_text text="object with 4 samples" />
127 <has_text text="Time range: 0.7-1139.9 seconds (0-19 minutes)" /> 116 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
128 <has_text text="Mass range: 50.0019-999.9863 m/z" /> 117 <has_text text="Mass range: 50.0021-999.9863 m/z" />
129 <has_text text="Peaks: 135846 (about 15094 per sample)" /> 118 <has_text text="Peaks: 59359 (about 14840 per sample)" />
130 <has_text text="Peak Groups: 0" /> 119 <has_text text="Peak Groups: 0" />
131 <has_text text="Sample classes: bio, blank" /> 120 <has_text text="Sample classes: bio, blank" />
132 </assert_contents> 121 </assert_contents>
133 </output> 122 </output>
134 </test> 123 </test>
135 </tests> 124 </tests>
136 125
137 <help><![CDATA[ 126 <help><![CDATA[
138
139 127
140 .. class:: infomark 128 @HELP_AUTHORS@
141
142 **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
143
144 .. class:: infomark
145
146 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]
147
148 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
149
150
151
152 ---------------------------------------------------
153 129
154 =========== 130 ===========
155 Xcms.retcor 131 Xcms.retcor
156 =========== 132 ===========
157 133
295 --------------------------------------------------- 271 ---------------------------------------------------
296 272
297 Changelog/News 273 Changelog/News
298 -------------- 274 --------------
299 275
276 **Version 2.0.6 - 04/04/2016**
277
278 - TEST: refactoring to pass planemo test using conda dependencies
279
280
300 **Version 2.0.5 - 10/02/2016** 281 **Version 2.0.5 - 10/02/2016**
301 282
302 - BUGFIX: better management of errors. Datasets remained green although the process failed 283 - BUGFIX: better management of errors. Datasets remained green although the process failed
303 284
304 - BUGFIX: some pdf remained empty even when the process succeed 285 - BUGFIX: some pdf remained empty even when the process succeed
315 - IMPROVEMENT: parameter labels have changed to facilitate their reading. 296 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
316 297
317 298
318 ]]></help> 299 ]]></help>
319 300
320 <citations> 301
321 <citation type="doi">10.1021/ac051437y</citation> 302 <expand macro="citation" />
322 <citation type="doi">10.1093/bioinformatics/btu813</citation>
323 </citations>
324 303
325 </tool> 304 </tool>