Mercurial > repos > workflow4metabolomics > xcms_refine
comparison macros_xcms.xml @ 1:20f8ebc3a391 draft
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author | workflow4metabolomics |
---|---|
date | Mon, 11 Sep 2023 09:19:47 +0000 |
parents | eb115eb8f25c |
children |
comparison
equal
deleted
inserted
replaced
0:eb115eb8f25c | 1:20f8ebc3a391 |
---|---|
1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <macros> | 2 <macros> |
3 | 3 |
4 <token name="@TOOL_VERSION@">3.12.0</token> | 4 <token name="@TOOL_VERSION@">3.12.0</token> |
5 <token name="@VERSION_SUFFIX@">1</token> | |
6 <token name="@PROFILE@">21.09</token> | |
5 <xml name="requirements"> | 7 <xml name="requirements"> |
6 <requirements> | 8 <requirements> |
7 <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement> | 9 <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement> |
8 <requirement type="package" version="1.1_5">r-batch</requirement> | 10 <requirement type="package" version="1.1_5">r-batch</requirement> |
9 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> | 11 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> |
15 <!-- FILE_LOAD for planemo test --> | 17 <!-- FILE_LOAD for planemo test --> |
16 <token name="@COMMAND_FILE_LOAD@"> | 18 <token name="@COMMAND_FILE_LOAD@"> |
17 #if $file_load_section.file_load_conditional.file_load_select == "yes": | 19 #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"): | 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"): |
19 #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) | 21 #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 ] ) | 22 #set singlefile_sampleName = '|'.join( [ str( $single_file.element_identifier ) for $single_file in $file_load_section.file_load_conditional.input ] ) |
21 | 23 |
22 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' | 24 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' |
23 #else | 25 #else |
24 zipfile '$file_load_section.file_load_conditional.input' | 26 zipfile '$file_load_section.file_load_conditional.input' |
25 #end if | 27 #end if |
34 <option value="yes" >yes</option> | 36 <option value="yes" >yes</option> |
35 </param> | 37 </param> |
36 <when value="no"> | 38 <when value="no"> |
37 </when> | 39 </when> |
38 <when value="yes"> | 40 <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." /> | 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." /> |
40 </when> | 42 </when> |
41 </conditional> | 43 </conditional> |
42 </section> | 44 </section> |
43 </xml> | 45 </xml> |
44 | 46 |
78 </section> | 80 </section> |
79 </xml> | 81 </xml> |
80 | 82 |
81 <!-- PEAKLIST --> | 83 <!-- PEAKLIST --> |
82 <token name="@COMMAND_PEAKLIST@"> | 84 <token name="@COMMAND_PEAKLIST@"> |
83 #if $peaklist.peaklistBool | 85 #if $peaklist.peaklistBool == 'true' |
84 convertRTMinute $peaklist.convertRTMinute | 86 convertRTMinute $peaklist.convertRTMinute |
85 numDigitsMZ $peaklist.numDigitsMZ | 87 numDigitsMZ $peaklist.numDigitsMZ |
86 numDigitsRT $peaklist.numDigitsRT | 88 numDigitsRT $peaklist.numDigitsRT |
87 intval $peaklist.intval | 89 intval $peaklist.intval |
88 naTOzero $peaklist.naTOzero | 90 naTOzero $peaklist.naTOzero |
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"/> | 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"/> |
102 </xml> | 104 </xml> |
103 | 105 |
104 <xml name="input_peaklist_section"> | 106 <xml name="input_peaklist_section"> |
105 <section name="peaklist" title="Peak List" expanded="True"> | 107 <section name="peaklist" title="Peak List" expanded="True"> |
106 <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" /> | 108 <param name="peaklistBool" type="hidden" label="Get the Peak List" value="true" /> |
107 <expand macro="input_peaklist"/> | 109 <expand macro="input_peaklist"/> |
108 </section> | 110 </section> |
109 </xml> | 111 </xml> |
110 | 112 |
111 <xml name="input_peaklist_conditional"> | 113 <xml name="input_peaklist_conditional"> |
112 <conditional name="peaklist"> | 114 <conditional name="peaklist"> |
113 <param name="peaklistBool" type="boolean" label="Get the Peak List" /> | 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> | |
114 <when value="true"> | 119 <when value="true"> |
115 <expand macro="input_peaklist"/> | 120 <expand macro="input_peaklist"/> |
116 </when> | 121 </when> |
117 <when value="false" /> | 122 <when value="false" /> |
118 </conditional> | 123 </conditional> |
119 </xml> | 124 </xml> |
120 | 125 |
121 <xml name="output_peaklist" token_function=""> | 126 <xml name="output_peaklist" token_function=""> |
122 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" > | 127 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" > |
123 <filter>(peaklist['peaklistBool'])</filter> | 128 <filter>peaklist['peaklistBool'] == 'true'</filter> |
124 </data> | 129 </data> |
125 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" > | 130 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" > |
126 <filter>(peaklist['peaklistBool'])</filter> | 131 <filter>peaklist['peaklistBool'] == 'true'</filter> |
127 </data> | 132 </data> |
128 </xml> | 133 </xml> |
129 | 134 |
130 <token name="@HELP_PEAKLIST@"> | 135 <token name="@HELP_PEAKLIST@"> |
131 | 136 |
241 For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_ | 246 For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_ |
242 | 247 |
243 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html | 248 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html |
244 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf | 249 .. _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 | 250 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html |
246 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS | 251 .. _news: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS |
247 | 252 |
248 </token> | 253 </token> |
249 | 254 |
250 <token name="@HELP_XCMS_NEWVERSION_3440@"> | 255 <token name="@HELP_XCMS_NEWVERSION_3440@"> |
251 **Version 3.4.4.0 - 08/02/2019** | 256 **Version 3.4.4.0 - 08/02/2019** |
252 | 257 |
253 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) | 258 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS news_) |
254 </token> | 259 </token> |
255 <token name="@HELP_XCMS_NEWVERSION_3610@"> | 260 <token name="@HELP_XCMS_NEWVERSION_3610@"> |
256 **Version 3.6.1+galaxy* - 03/09/2019** | 261 **Version 3.6.1+galaxy* - 03/09/2019** |
257 | 262 |
258 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_) | 263 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS news_) |
259 </token> | 264 </token> |
260 <token name="@HELP_XCMS_NEWVERSION_31200@"> | 265 <token name="@HELP_XCMS_NEWVERSION_31200@"> |
261 **Version 3.12.0+galaxy* - 03/03/2020** | 266 **Version 3.12.0+galaxy* - 03/03/2020** |
262 | 267 |
263 - UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_) | 268 - UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS news_) |
264 </token> | 269 </token> |
265 | 270 |
266 <xml name="citation"> | 271 <xml name="citation"> |
267 <citations> | 272 <citations> |
268 <citation type="doi">10.1021/ac051437y</citation> | 273 <citation type="doi">10.1021/ac051437y</citation> |