Mercurial > repos > lecorguille > xcms_xcmsset

comparison abims_xcms_xcmsSet.xml @ 16:f28041d2180a draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
author lecorguille
date Mon, 30 Jan 2017 08:51:01 -0500
parents 1a9bbd4670e8
children 602acc32b549
comparison
equal deleted inserted replaced
15:1a9bbd4670e8 16:f28041d2180a
1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.10"> 1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.11">
2 2
3 <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description> 3 <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
4 4
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
22 xsetRdataOutput $xsetRData 22 xsetRdataOutput $xsetRData
23 sampleMetadataOutput $sampleMetadata 23 sampleMetadataOutput $sampleMetadata
24 ticspdf $ticsRawPdf 24 ticspdf $ticsRawPdf
25 bicspdf $bpcsRawPdf 25 bicspdf $bpcsRawPdf
26 26
27
28 #if $options_scanrange.option == "show":
29 scanrange "c($options_scanrange.scanrange)"
30 #end if
31
27 ## profmethod $profmethod 32 ## profmethod $profmethod
28 nSlaves \${GALAXY_SLOTS:-1} method $methods.method 33 nSlaves \${GALAXY_SLOTS:-1} method $methods.method
29 #if $methods.method == "centWave": 34 #if $methods.method == "centWave":
30 ppm $methods.ppm 35 ppm $methods.ppm
31 peakwidth "c($methods.peakwidth)" 36 peakwidth "c($methods.peakwidth)"
32 #if $methods.options_scanrange.option == "show":
33 scanrange "c($methods.options_scanrange.scanrange)"
34 #end if
35 #if $methods.options_c.option == "show": 37 #if $methods.options_c.option == "show":
36 mzdiff $methods.options_c.mzdiff 38 mzdiff $methods.options_c.mzdiff
37 snthresh $methods.options_c.snthresh 39 snthresh $methods.options_c.snthresh
38 integrate $methods.options_c.integrate 40 integrate $methods.options_c.integrate
39 noise $methods.options_c.noise 41 noise $methods.options_c.noise
77 </param> 79 </param>
78 </when> 80 </when>
79 81
80 </conditional> 82 </conditional>
81 83
84 <conditional name="options_scanrange">
85 <param name="option" type="select" label="Scan range option " >
86 <option value="show">show</option>
87 <option value="hide" selected="true">hide</option>
88 </param>
89 <when value="show">
90 <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
91 <validator type="empty_field"/>
92 </param>
93 </when>
94 <when value="hide">
95 </when>
96 </conditional>
97
82 98
83 <!-- 99 <!--
84 <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" > 100 <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >
85 <option value="bin" selected="true">bin</option> 101 <option value="bin" selected="true">bin</option>
86 <option value="binlin">binlin</option> 102 <option value="binlin">binlin</option>
98 114
99 <!-- centWave Filter options --> 115 <!-- centWave Filter options -->
100 <when value="centWave"> 116 <when value="centWave">
101 <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" /> 117 <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" />
102 <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" /> 118 <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" />
103 <conditional name="options_scanrange"> 119
104 <param name="option" type="select" label="Scan range option " >
105 <option value="show">show</option>
106 <option value="hide" selected="true">hide</option>
107 </param>
108 <when value="show">
109 <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
110 <validator type="empty_field"/>
111 </param>
112 </when>
113 <when value="hide">
114 </when>
115 </conditional>
116
117 <conditional name="options_c"> 120 <conditional name="options_c">
118 <param name="option" type="select" label="Advanced options" > 121 <param name="option" type="select" label="Advanced options" >
119 <option value="show">show</option> 122 <option value="show">show</option>
120 <option value="hide" selected="true">hide</option> 123 <option value="hide" selected="true">hide</option>
121 </param> 124 </param>
132 <when value="hide"> 135 <when value="hide">
133 </when> 136 </when>
134 </conditional> 137 </conditional>
135 </when> 138 </when>
136 139
137 <!-- matched Filter options --> 140 <!-- matched Filter options -->
138 <when value="matchedFilter"> 141 <when value="matchedFilter">
139 <param name="step" type="float" value="0.01" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" /> 142 <param name="step" type="float" value="0.01" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" />
140 <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" /> 143 <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" />
141 <conditional name="options_m"> 144 <conditional name="options_m">
142 <param name="option" type="select" label="Advanced options" > 145 <param name="option" type="select" label="Advanced options" >
157 <when value="hide"> 160 <when value="hide">
158 </when> 161 </when>
159 </conditional> 162 </conditional>
160 </when> 163 </when>
161 164
162 <!-- MSW Filter options --> 165 <!-- MSW Filter options -->
163 <when value="MSW"> 166 <when value="MSW">
164 <param name="nearbyPeak" type="select" label="Determine whether to include the nearby small peaks of major peaks" help="[nearbyPeak]" > 167 <param name="nearbyPeak" type="select" label="Determine whether to include the nearby small peaks of major peaks" help="[nearbyPeak]" >
165 <option value="TRUE">TRUE</option> 168 <option value="TRUE">TRUE</option>
166 <option value="FALSE">FALSE</option> 169 <option value="FALSE">FALSE</option>
167 </param> 170 </param>
473 --------------------------------------------------- 476 ---------------------------------------------------
474 477
475 Changelog/News 478 Changelog/News
476 -------------- 479 --------------
477 480
481 **Version 2.0.11 - 22/12/2016**
482
483 - BUGFIX: propose scanrange for all methods
484
478 **Version 2.0.10 - 22/12/2016** 485 **Version 2.0.10 - 22/12/2016**
479 486
480 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph 487 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
481 488
482 **Version 2.0.9 - 06/07/2016** 489 **Version 2.0.9 - 06/07/2016**