Mercurial > repos > lecorguille > xcms_plot_chromatogram

comparison macros_xcms.xml @ 3:d8df8bd6e132 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 878be1bfbe93af0a140df76fa47f0a82a48189e3
author lecorguille
date Tue, 09 Oct 2018 04:37:28 -0400
parents c749bfd3410e
children 7c0cc7a3c3db
comparison
equal deleted inserted replaced
2:2130b2a6d12c 3:d8df8bd6e132
88 naTOzero $peaklist.naTOzero 88 naTOzero $peaklist.naTOzero
89 #end if 89 #end if
90 </token> 90 </token>
91 91
92 <xml name="input_peaklist"> 92 <xml name="input_peaklist">
93 <conditional name="peaklist">
94 <param name="peaklistBool" type="boolean" label="Get a Peak List" />
95 <when value="true">
96 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> 93 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
97 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> 94 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
98 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> 95 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
99 <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">
100 <option value="into" selected="true">into</option> 97 <option value="into" selected="true">into</option>
101 <option value="maxo">maxo</option> 98 <option value="maxo">maxo</option>
102 <option value="intb">intb</option> 99 <option value="intb">intb</option>
103 </param> 100 </param>
104 <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="Replace the remain NA by 0 in the dataMatrix" help="Rather mandatory for some downstream statistical steps"/>
102 </xml>
103
104 <xml name="input_peaklist_section">
105 <section name="peaklist" title="Peak List" expanded="True">
106 <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" />
107 <expand macro="input_peaklist"/>
108 </section>
109 </xml>
110
111 <xml name="input_peaklist_conditional">
112 <conditional name="peaklist">
113 <param name="peaklistBool" type="boolean" label="Get the Peak List" />
114 <when value="true">
115 <expand macro="input_peaklist"/>
105 </when> 116 </when>
106 <when value="false" /> 117 <when value="false" />
107 </conditional> 118 </conditional>
108 </xml> 119 </xml>
109 120