Mercurial > repos > workflow4metabolomics > xcms_refine

comparison macros_xcms.xml @ 0:eb115eb8f25c 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 d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
author workflow4metabolomics
date Thu, 17 Jun 2021 07:42:55 +0000
parents
children 20f8ebc3a391
comparison
equal deleted inserted replaced
-1:000000000000 0:eb115eb8f25c
1 <?xml version="1.0"?>
2 <macros>
3
4 <token name="@TOOL_VERSION@">3.12.0</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
8 <requirement type="package" version="1.1_5">r-batch</requirement>
9 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
10 <requirement type="package" version="6.0">unzip</requirement>
11 <yield />
12 </requirements>
13 </xml>
14
15 <!-- FILE_LOAD for planemo test -->
16 <token name="@COMMAND_FILE_LOAD@">
17 #if $file_load_section.file_load_conditional.file_load_select == "yes":
18 #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
19 #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
20 #set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
21
22 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
23 #else
24 zipfile '$file_load_section.file_load_conditional.input'
25 #end if
26 #end if
27 </token>
28
29 <xml name="input_file_load">
30 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
31 <conditional name="file_load_conditional">
32 <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message saying that your original dataset or zip file have been deleted on the server." >
33 <option value="no" >no need</option>
34 <option value="yes" >yes</option>
35 </param>
36 <when value="no">
37 </when>
38 <when value="yes">
39 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
40 </when>
41 </conditional>
42 </section>
43 </xml>
44
45 <xml name="test_file_load_zip">
46 <section name="file_load_section">
47 <conditional name="file_load_conditional">
48 <param name="file_load_select" value="yes" />
49 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
50 </conditional>
51 </section>
52 </xml>
53
54 <xml name="test_file_load_zip_sacuri">
55 <section name="file_load_section">
56 <conditional name="file_load_conditional">
57 <param name="file_load_select" value="yes" />
58 <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
59 </conditional>
60 </section>
61 </xml>
62
63 <xml name="test_file_load_single">
64 <section name="file_load_section">
65 <conditional name="file_load_conditional">
66 <param name="file_load_select" value="yes" />
67 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
68 </conditional>
69 </section>
70 </xml>
71
72 <xml name="test_file_load_single_file" token_filename="">
73 <section name="file_load_section">
74 <conditional name="file_load_conditional">
75 <param name="file_load_select" value="yes" />
76 <param name="input" value="@FILENAME@.CDF" ftype="netcdf" />
77 </conditional>
78 </section>
79 </xml>
80
81 <!-- PEAKLIST -->
82 <token name="@COMMAND_PEAKLIST@">
83 #if $peaklist.peaklistBool
84 convertRTMinute $peaklist.convertRTMinute
85 numDigitsMZ $peaklist.numDigitsMZ
86 numDigitsRT $peaklist.numDigitsRT
87 intval $peaklist.intval
88 naTOzero $peaklist.naTOzero
89 #end if
90 </token>
91
92 <xml name="input_peaklist">
93 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
94 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
95 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
96 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
97 <option value="into" selected="true">into</option>
98 <option value="maxo">maxo</option>
99 <option value="intb">intb</option>
100 </param>
101 <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="If NA values remain, replace them by 0 in the dataMatrix" help="Mandatory for some of the downstream tools (data processing, statistics) that do not accept NA values"/>
102 </xml>
103
104 <xml name="input_peaklist_section">
105 <section name="peaklist" title="Peak List" expanded="True">
106 <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" />
107 <expand macro="input_peaklist"/>
108 </section>
109 </xml>
110
111 <xml name="input_peaklist_conditional">
112 <conditional name="peaklist">
113 <param name="peaklistBool" type="boolean" label="Get the Peak List" />
114 <when value="true">
115 <expand macro="input_peaklist"/>
116 </when>
117 <when value="false" />
118 </conditional>
119 </xml>
120
121 <xml name="output_peaklist" token_function="">
122 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" >
123 <filter>(peaklist['peaklistBool'])</filter>
124 </data>
125 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" >
126 <filter>(peaklist['peaklistBool'])</filter>
127 </data>
128 </xml>
129
130 <token name="@HELP_PEAKLIST@">
131
132 Get a Peak List
133 ---------------
134
135 If 'true', the module generates two additional files corresponding to the peak list:
136 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
137 - the data matrix (corresponding to related intensities)
138
139 **decimal places for [mass or retention time] values in identifiers**
140
141 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
142 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
143 | Theses parameters do not affect decimal places in columns other than the identifier one.
144
145 **Reported intensity values**
146
147 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
148 | - into: integrated area of original (raw) peak
149 | - maxo: maximum intensity of original (raw) peak
150 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
151
152 </token>
153
154 <token name="@HELP_PEAKLIST_OUTPUT@">
155 xset.variableMetadata.tsv : tabular format
156
157 | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
158
159 xset.dataMatrix.tsv : tabular format
160
161 | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
162 </token>
163
164 <!-- CENTWAVE -->
165 <token name="@COMMAND_CENTWAVE@">
166 ppm $methods.ppm
167 peakwidth "c($methods.peakwidth)"
168
169 ## Advanced
170 snthresh $methods.CentWaveAdv.snthresh
171 prefilter "c($methods.CentWaveAdv.prefilter)"
172 mzCenterFun $methods.CentWaveAdv.mzCenterFun
173 integrate $methods.CentWaveAdv.integrate
174 mzdiff $methods.CentWaveAdv.mzdiff
175 fitgauss $methods.CentWaveAdv.fitgauss
176 noise $methods.CentWaveAdv.noise
177 verboseColumns $methods.CentWaveAdv.verboseColumns
178 </token>
179
180 <xml name="input_centwave">
181 <param argument="ppm" type="float" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="for the initial ROI definition." />
182 <param argument="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="with the expected approximate peak width in chromatographic space.">
183 <expand macro="input_validator_range_float"/>
184 </param>
185 </xml>
186
187 <xml name="input_centwaveAdv">
188 <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" />
189 <param argument="prefilter" type="text" value="3,100" label="Prefilter step for for the first analysis step (ROI detection)" help="Separate by coma k, I. Mass traces are only retained if they contain at least ‘k‘ peaks with intensity ‘>= I‘.">
190 <expand macro="input_validator_range_integer"/>
191 </param>
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>
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>
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>
198 </param>
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>
201 <option value="2">peak limits based on real data (more accurate but prone to noise)</option>
202 </param>
203 <param argument="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping retention times" help="can be negative to allow overlap" />
204 <param argument="fitgauss" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="fitgauss" help="whether or not a Gaussian should be fitted to each peak" />
205 <param argument="noise" type="integer" value="0" label="Noise filter" help="allowing to set a minimum intensity required for centroids to be considered in the first analysis step (centroids with intensity lower than ‘noise’ are omitted from ROI detection)." />
206 <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" />
207 </xml>
208
209 <token name="@COMMAND_CENTWAVEADVROI@">
210 #if $sectionROI.roiList:
211 roiList '$sectionROI.roiList'
212 firstBaselineCheck $sectionROI.firstBaselineCheck
213 #if $sectionROI.roiScales != "":
214 roiScales "c($sectionROI.roiScales)"
215 #end if
216 #end if
217 </token>
218
219 <xml name="input_centwaveAdvROI" token_optional="true">
220 <param argument="roiList" type="data" format="tabular" optional="@OPTIONAL@" label="List of regions-of-interest (ROI) representing detected mass traces" help="If ROIs are submitted the first analysis step is omitted and chromatographic peak detection is performed on the submitted ROIs. Each ROI is expected to have the following elements specified: ‘scmin’ (start scan index), ‘scmax’ (end scan index), ‘mzmin’ (minimum m/z), ‘mzmax’ (maximum m/z), ‘length’ (number of scans), ‘intensity’ (summed intensity)." />
221 <param argument="firstBaselineCheck" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Is continuous data within regions of interest is checked to be above the first baseline." />
222 <param argument="roiScales" type="text" value="" optional="true" label="Numeric vector defining the scale for each region of interest in ‘roiList’" help="Length equal to ‘roiList’ - Should be used for the centWave-wavelets (format 0.9,1,0.2)">
223 <expand macro="input_validator_range_float"/>
224 </param>
225 </xml>
226
227 <!-- MISC -->
228 <token name="@HELP_AUTHORS@">
229 .. class:: infomark
230
231 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
232
233 @HELP_AUTHORS_WRAPPERS@
234
235 ---------------------------------------------------
236
237 </token>
238
239 <token name="@HELP_XCMS_MANUAL@">
240
241 For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_
242
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
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
247
248 </token>
249
250 <token name="@HELP_XCMS_NEWVERSION_3440@">
251 **Version 3.4.4.0 - 08/02/2019**
252
253 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
254 </token>
255 <token name="@HELP_XCMS_NEWVERSION_3610@">
256 **Version 3.6.1+galaxy* - 03/09/2019**
257
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_)
264 </token>
265
266 <xml name="citation">
267 <citations>
268 <citation type="doi">10.1021/ac051437y</citation>
269 <expand macro="citation_w4m"/>
270 </citations>
271 </xml>
272 </macros>