Mercurial > repos > lecorguille > msnbase_readmsdata
comparison macros_xcms.xml @ 15:7faf9b2d83f6 draft
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author | workflow4metabolomics |
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date | Mon, 11 Sep 2023 09:24:51 +0000 |
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14:11ab2081bd4a | 15:7faf9b2d83f6 |
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1 <?xml version="1.0"?> | |
2 <macros> | |
3 | |
4 <token name="@TOOL_VERSION@">3.12.0</token> | |
5 <token name="@VERSION_SUFFIX@">1</token> | |
6 <token name="@PROFILE@">21.09</token> | |
7 <xml name="requirements"> | |
8 <requirements> | |
9 <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement> | |
10 <requirement type="package" version="1.1_5">r-batch</requirement> | |
11 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> | |
12 <requirement type="package" version="6.0">unzip</requirement> | |
13 <yield /> | |
14 </requirements> | |
15 </xml> | |
16 | |
17 <!-- FILE_LOAD for planemo test --> | |
18 <token name="@COMMAND_FILE_LOAD@"> | |
19 #if $file_load_section.file_load_conditional.file_load_select == "yes": | |
20 #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"): | |
21 #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) | |
22 #set singlefile_sampleName = '|'.join( [ str( $single_file.element_identifier ) for $single_file in $file_load_section.file_load_conditional.input ] ) | |
23 | |
24 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' | |
25 #else | |
26 zipfile '$file_load_section.file_load_conditional.input' | |
27 #end if | |
28 #end if | |
29 </token> | |
30 | |
31 <xml name="input_file_load"> | |
32 <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> | |
33 <conditional name="file_load_conditional"> | |
34 <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." > | |
35 <option value="no" >no need</option> | |
36 <option value="yes" >yes</option> | |
37 </param> | |
38 <when value="no"> | |
39 </when> | |
40 <when value="yes"> | |
41 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,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: zip. See the help section below." /> | |
42 </when> | |
43 </conditional> | |
44 </section> | |
45 </xml> | |
46 | |
47 <xml name="test_file_load_zip"> | |
48 <section name="file_load_section"> | |
49 <conditional name="file_load_conditional"> | |
50 <param name="file_load_select" value="yes" /> | |
51 <param name="input" value="faahKO_reduce.zip" ftype="zip" /> | |
52 </conditional> | |
53 </section> | |
54 </xml> | |
55 | |
56 <xml name="test_file_load_zip_sacuri"> | |
57 <section name="file_load_section"> | |
58 <conditional name="file_load_conditional"> | |
59 <param name="file_load_select" value="yes" /> | |
60 <param name="input" value="sacuri_dir_root.zip" ftype="zip" /> | |
61 </conditional> | |
62 </section> | |
63 </xml> | |
64 | |
65 <xml name="test_file_load_single"> | |
66 <section name="file_load_section"> | |
67 <conditional name="file_load_conditional"> | |
68 <param name="file_load_select" value="yes" /> | |
69 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> | |
70 </conditional> | |
71 </section> | |
72 </xml> | |
73 | |
74 <xml name="test_file_load_single_file" token_filename=""> | |
75 <section name="file_load_section"> | |
76 <conditional name="file_load_conditional"> | |
77 <param name="file_load_select" value="yes" /> | |
78 <param name="input" value="@FILENAME@.CDF" ftype="netcdf" /> | |
79 </conditional> | |
80 </section> | |
81 </xml> | |
82 | |
83 <!-- PEAKLIST --> | |
84 <token name="@COMMAND_PEAKLIST@"> | |
85 #if $peaklist.peaklistBool == 'true' | |
86 convertRTMinute $peaklist.convertRTMinute | |
87 numDigitsMZ $peaklist.numDigitsMZ | |
88 numDigitsRT $peaklist.numDigitsRT | |
89 intval $peaklist.intval | |
90 naTOzero $peaklist.naTOzero | |
91 #end if | |
92 </token> | |
93 | |
94 <xml name="input_peaklist"> | |
95 <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"/> | |
96 <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" /> | |
97 <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" /> | |
98 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> | |
99 <option value="into" selected="true">into</option> | |
100 <option value="maxo">maxo</option> | |
101 <option value="intb">intb</option> | |
102 </param> | |
103 <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"/> | |
104 </xml> | |
105 | |
106 <xml name="input_peaklist_section"> | |
107 <section name="peaklist" title="Peak List" expanded="True"> | |
108 <param name="peaklistBool" type="hidden" label="Get the Peak List" value="true" /> | |
109 <expand macro="input_peaklist"/> | |
110 </section> | |
111 </xml> | |
112 | |
113 <xml name="input_peaklist_conditional"> | |
114 <conditional name="peaklist"> | |
115 <param name="peaklistBool" type="select" label="Get the Peak List"> | |
116 <option value="true">Yes</option> | |
117 <option value="false">No</option> | |
118 </param> | |
119 <when value="true"> | |
120 <expand macro="input_peaklist"/> | |
121 </when> | |
122 <when value="false" /> | |
123 </conditional> | |
124 </xml> | |
125 | |
126 <xml name="output_peaklist" token_function=""> | |
127 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" > | |
128 <filter>peaklist['peaklistBool'] == 'true'</filter> | |
129 </data> | |
130 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" > | |
131 <filter>peaklist['peaklistBool'] == 'true'</filter> | |
132 </data> | |
133 </xml> | |
134 | |
135 <token name="@HELP_PEAKLIST@"> | |
136 | |
137 Get a Peak List | |
138 --------------- | |
139 | |
140 If 'true', the module generates two additional files corresponding to the peak list: | |
141 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time) | |
142 - the data matrix (corresponding to related intensities) | |
143 | |
144 **decimal places for [mass or retention time] values in identifiers** | |
145 | |
146 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time. | |
147 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively. | |
148 | Theses parameters do not affect decimal places in columns other than the identifier one. | |
149 | |
150 **Reported intensity values** | |
151 | |
152 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter: | |
153 | - into: integrated area of original (raw) peak | |
154 | - maxo: maximum intensity of original (raw) peak | |
155 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’) | |
156 | |
157 </token> | |
158 | |
159 <token name="@HELP_PEAKLIST_OUTPUT@"> | |
160 xset.variableMetadata.tsv : tabular format | |
161 | |
162 | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter** modules. | |
163 | |
164 xset.dataMatrix.tsv : tabular format | |
165 | |
166 | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter** modules. | |
167 </token> | |
168 | |
169 <!-- CENTWAVE --> | |
170 <token name="@COMMAND_CENTWAVE@"> | |
171 ppm $methods.ppm | |
172 peakwidth "c($methods.peakwidth)" | |
173 | |
174 ## Advanced | |
175 snthresh $methods.CentWaveAdv.snthresh | |
176 prefilter "c($methods.CentWaveAdv.prefilter)" | |
177 mzCenterFun $methods.CentWaveAdv.mzCenterFun | |
178 integrate $methods.CentWaveAdv.integrate | |
179 mzdiff $methods.CentWaveAdv.mzdiff | |
180 fitgauss $methods.CentWaveAdv.fitgauss | |
181 noise $methods.CentWaveAdv.noise | |
182 verboseColumns $methods.CentWaveAdv.verboseColumns | |
183 </token> | |
184 | |
185 <xml name="input_centwave"> | |
186 <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." /> | |
187 <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."> | |
188 <expand macro="input_validator_range_float"/> | |
189 </param> | |
190 </xml> | |
191 | |
192 <xml name="input_centwaveAdv"> | |
193 <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" /> | |
194 <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‘."> | |
195 <expand macro="input_validator_range_integer"/> | |
196 </param> | |
197 <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" > | |
198 <option value="wMean">intensity weighted mean of the peak's m/z values</option> | |
199 <option value="mean">mean of the peak's m/z values</option> | |
200 <option value="apex">use the m/z value at the peak apex</option> | |
201 <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> | |
202 <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option> | |
203 </param> | |
204 <param argument="integrate" type="select" label="Integration method" > | |
205 <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option> | |
206 <option value="2">peak limits based on real data (more accurate but prone to noise)</option> | |
207 </param> | |
208 <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" /> | |
209 <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" /> | |
210 <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)." /> | |
211 <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" /> | |
212 </xml> | |
213 | |
214 <token name="@COMMAND_CENTWAVEADVROI@"> | |
215 #if $sectionROI.roiList: | |
216 roiList '$sectionROI.roiList' | |
217 firstBaselineCheck $sectionROI.firstBaselineCheck | |
218 #if $sectionROI.roiScales != "": | |
219 roiScales "c($sectionROI.roiScales)" | |
220 #end if | |
221 #end if | |
222 </token> | |
223 | |
224 <xml name="input_centwaveAdvROI" token_optional="true"> | |
225 <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)." /> | |
226 <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." /> | |
227 <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)"> | |
228 <expand macro="input_validator_range_float"/> | |
229 </param> | |
230 </xml> | |
231 | |
232 <!-- MISC --> | |
233 <token name="@HELP_AUTHORS@"> | |
234 .. class:: infomark | |
235 | |
236 **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 | |
237 | |
238 @HELP_AUTHORS_WRAPPERS@ | |
239 | |
240 --------------------------------------------------- | |
241 | |
242 </token> | |
243 | |
244 <token name="@HELP_XCMS_MANUAL@"> | |
245 | |
246 For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_ | |
247 | |
248 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html | |
249 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf | |
250 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html | |
251 .. _news: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS | |
252 | |
253 </token> | |
254 | |
255 <token name="@HELP_XCMS_NEWVERSION_3440@"> | |
256 **Version 3.4.4.0 - 08/02/2019** | |
257 | |
258 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS news_) | |
259 </token> | |
260 <token name="@HELP_XCMS_NEWVERSION_3610@"> | |
261 **Version 3.6.1+galaxy* - 03/09/2019** | |
262 | |
263 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS news_) | |
264 </token> | |
265 <token name="@HELP_XCMS_NEWVERSION_31200@"> | |
266 **Version 3.12.0+galaxy* - 03/03/2020** | |
267 | |
268 - UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS news_) | |
269 </token> | |
270 | |
271 <xml name="citation"> | |
272 <citations> | |
273 <citation type="doi">10.1021/ac051437y</citation> | |
274 <expand macro="citation_w4m"/> | |
275 </citations> | |
276 </xml> | |
277 </macros> |