Mercurial > repos > lecorguille > xcms_plot_chromatogram

comparison macros_xcms.xml @ 14:8846a03995d3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:18:38 +0000
parents 024974037c4e
children
comparison
equal deleted inserted replaced
13:024974037c4e 14:8846a03995d3
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>