Mercurial > repos > lecorguille > xcms_export_samplemetadata

comparison macros_xcms.xml @ 9:94eb263cfab4 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 dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author workflow4metabolomics
date Wed, 07 Apr 2021 09:53:54 +0000
parents c684ccd89267
children cdab04a1d1d7
comparison
equal deleted inserted replaced
8:c684ccd89267 9:94eb263cfab4
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 3
4 <token name="@TOOL_VERSION@">3.6.1</token> 4 <token name="@TOOL_VERSION@">3.12.0</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
8 <requirement type="package" version="1.1_5">r-batch</requirement> 8 <requirement type="package" version="1.1_5">r-batch</requirement>
9 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> 9 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
96 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> 96 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
97 <option value="into" selected="true">into</option> 97 <option value="into" selected="true">into</option>
98 <option value="maxo">maxo</option> 98 <option value="maxo">maxo</option>
99 <option value="intb">intb</option> 99 <option value="intb">intb</option>
100 </param> 100 </param>
101 <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Replace the remain NA by 0 in the dataMatrix" help="Rather mandatory for some downstream statistical steps"/> 101 <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="If NA values remain, replace them by 0 in the dataMatrix" help="Mandatory for some of the downstream tools (data processing, statistics) that do not accept NA values"/>
102 </xml> 102 </xml>
103 103
104 <xml name="input_peaklist_section"> 104 <xml name="input_peaklist_section">
105 <section name="peaklist" title="Peak List" expanded="True"> 105 <section name="peaklist" title="Peak List" expanded="True">
106 <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" /> 106 <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" />
191 </param> 191 </param>
192 <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" > 192 <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" >
193 <option value="wMean">intensity weighted mean of the peak's m/z values</option> 193 <option value="wMean">intensity weighted mean of the peak's m/z values</option>
194 <option value="mean">mean of the peak's m/z values</option> 194 <option value="mean">mean of the peak's m/z values</option>
195 <option value="apex">use the m/z value at the peak apex</option> 195 <option value="apex">use the m/z value at the peak apex</option>
196 <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option> 196 <option value="wMeanApex3">intensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
197 <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option> 197 <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option>
198 </param> 198 </param>
199 <param argument="integrate" type="select" label="Integration method" > 199 <param argument="integrate" type="select" label="Integration method" >
200 <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option> 200 <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option>
201 <option value="2">peak limits based on real data (more accurate but prone to noise)</option> 201 <option value="2">peak limits based on real data (more accurate but prone to noise)</option>
241 For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_ 241 For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_
242 242
243 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html 243 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
244 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf 244 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
245 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html 245 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
246 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
246 247
247 </token> 248 </token>
248 249
249 <token name="@HELP_XCMS_NEWVERSION_3440@"> 250 <token name="@HELP_XCMS_NEWVERSION_3440@">
250 **Version 3.4.4.0 - 08/02/2019** 251 **Version 3.4.4.0 - 08/02/2019**
253 </token> 254 </token>
254 <token name="@HELP_XCMS_NEWVERSION_3610@"> 255 <token name="@HELP_XCMS_NEWVERSION_3610@">
255 **Version 3.6.1+galaxy* - 03/09/2019** 256 **Version 3.6.1+galaxy* - 03/09/2019**
256 257
257 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_) 258 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
259 </token>
260 <token name="@HELP_XCMS_NEWVERSION_31200@">
261 **Version 3.12.0+galaxy* - 03/03/2020**
262
263 - UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_)
258 </token> 264 </token>
259 265
260 <xml name="citation"> 266 <xml name="citation">
261 <citations> 267 <citations>
262 <citation type="doi">10.1021/ac051437y</citation> 268 <citation type="doi">10.1021/ac051437y</citation>