Mercurial > repos > lecorguille > xcms_retcor

comparison abims_xcms_retcor.xml @ 8:4bfef820569b draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author lecorguille
date Fri, 07 Apr 2017 07:36:24 -0400
parents bb602a5b8819
children e4e0254a3c0a
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7:bb602a5b8819 8:4bfef820569b
1 <tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.8"> 1 <tool id="abims_xcms_retcor" name="xcms.retcor" version="2.1.0">
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 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 <expand macro="requirements"/>
10 <expand macro="stdio"/> 10 <expand macro="stdio"/>
11 11
12 <command><![CDATA[ 12 <command><![CDATA[
13 @COMMAND_XCMS_SCRIPT@ 13 @COMMAND_XCMS_SCRIPT@
14 image $image 14 image '$image'
15 xfunction retcor 15 xfunction retcor
16 16
17 xsetRdataOutput $xsetRData 17 xsetRdataOutput '$xsetRData'
18 ticspdf $ticsCorPdf 18 ticspdf '$ticsCorPdf'
19 bicspdf $bpcsCorPdf 19 bicspdf '$bpcsCorPdf'
20 rplotspdf $rplotsPdf 20 rplotspdf '$rplotsPdf'
21 21
22 method $methods.method 22 method $methods.method
23 #if $methods.method == "obiwarp": 23 #if $methods.method == "obiwarp":
24 profStep $methods.profStep 24 profStep $methods.profStep
25 #else 25 #else
31 family $methods.options.family 31 family $methods.options.family
32 plottype $methods.options.plottype 32 plottype $methods.options.plottype
33 #end if 33 #end if
34 #end if 34 #end if
35 35
36 @COMMAND_ZIPFILE_LOAD@ 36 @COMMAND_FILE_LOAD@
37 37
38 @COMMAND_LOG_EXIT@ 38 @COMMAND_LOG_EXIT@
39 ]]></command> 39 ]]></command>
40 40
41 <inputs> 41 <inputs>
42 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> 42 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
43 <conditional name="methods"> 43 <conditional name="methods">
44 <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" > 44 <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" >
45 <option value="obiwarp" >obiwarp</option> 45 <option value="obiwarp" >obiwarp</option>
46 <option value="peakgroups" selected="peakgroups">peakgroups</option> 46 <option value="peakgroups" selected="true">peakgroups</option>
47 </param> 47 </param>
48 <when value="obiwarp"> 48 <when value="obiwarp">
49 <param name="profStep" type="float" value="1" label="Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files" /> 49 <param name="profStep" type="float" value="1" label="Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files" />
50 </when> 50 </when>
51 <when value="peakgroups"> 51 <when value="peakgroups">
80 </when> 80 </when>
81 </conditional> 81 </conditional>
82 </when> 82 </when>
83 </conditional> 83 </conditional>
84 84
85 <expand macro="zipfile_load"/> 85 <expand macro="input_file_load"/>
86 86
87 </inputs> 87 </inputs>
88 88
89 <outputs> 89 <outputs>
90 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" /> 90 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" />
131 <param name="methods|missing" value="1"/> 131 <param name="methods|missing" value="1"/>
132 <param name="methods|options|option" value="show"/> 132 <param name="methods|options|option" value="show"/>
133 <param name="methods|options|span" value="0.2"/> 133 <param name="methods|options|span" value="0.2"/>
134 <param name="methods|options|family" value="gaussian"/> 134 <param name="methods|options|family" value="gaussian"/>
135 <param name="methods|options|plottype" value="deviation"/> 135 <param name="methods|options|plottype" value="deviation"/>
136 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> 136 <expand macro="test_file_load_zip"/>
137 <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> 137 <output name="log">
138 <assert_contents>
139 <has_text text="object with 4 samples" />
140 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
141 <has_text text="Mass range: 200.1-600 m/z" />
142 <has_text text="Peaks: 9251 (about 2313 per sample)" />
143 <has_text text="Peak Groups: 0" />
144 <has_text text="Sample classes: KO, WT" />
145 </assert_contents>
146 </output>
147 </test>
148 <test>
149 <param name="image" value="faahKO-single-class.xset.group.RData"/>
150 <param name="methods|method" value="peakgroups"/>
151 <param name="methods|smooth" value="loess"/>
152 <param name="methods|extra" value="1"/>
153 <param name="methods|missing" value="1"/>
154 <param name="methods|options|option" value="show"/>
155 <param name="methods|options|span" value="0.2"/>
156 <param name="methods|options|family" value="gaussian"/>
157 <param name="methods|options|plottype" value="deviation"/>
158 <expand macro="test_file_load_single"/>
138 <output name="log"> 159 <output name="log">
139 <assert_contents> 160 <assert_contents>
140 <has_text text="object with 4 samples" /> 161 <has_text text="object with 4 samples" />
141 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" /> 162 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
142 <has_text text="Mass range: 200.1-600 m/z" /> 163 <has_text text="Mass range: 200.1-600 m/z" />
296 --------------------------------------------------- 317 ---------------------------------------------------
297 318
298 Changelog/News 319 Changelog/News
299 -------------- 320 --------------
300 321
322 **Version 2.1.0 - 03/02/2017**
323
324 - IMPROVEMENT: xcms.retcor can deal with merged individual data
325
301 **Version 2.0.8 - 22/12/2016** 326 **Version 2.0.8 - 22/12/2016**
302 327
303 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph 328 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
304 329
305 **Version 2.0.7 - 06/07/2016** 330 **Version 2.0.7 - 06/07/2016**