comparison macros_xcms.xml @ 25:a066b8581b97 draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"
author workflow4metabolomics
date Tue, 28 Apr 2020 09:34:27 -0400
parents 761913919c21
children d45a786cbc40
comparison
equal deleted inserted replaced
24:761913919c21 25:a066b8581b97
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>