xcms_fillpeaks: macros_xcms.xml comparison

comparison macros_xcms.xml @ 46:871ffc15a6da draft

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253

author	workflow4metabolomics
date	Mon, 15 Jul 2024 15:52:02 +0000
parents	1a711c1b8b1f
children	1241183c8ae0

comparison

equal deleted inserted replaced

-:1a711c1b8b1f
+:871ffc15a6da
 <?xml version="1.0"?>
 <macros>
 <token name="@TOOL_VERSION@">3.12.0</token>
+<token name="@VERSION_SUFFIX@">1</token>
+<token name="@PROFILE@">21.09</token>
 <xml name="requirements">
 <requirements>
 <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
 <requirement type="package" version="1.1_5">r-batch</requirement>
 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
 <!-- FILE_LOAD for planemo test -->
 <token name="@COMMAND_FILE_LOAD@">
 #if $file_load_section.file_load_conditional.file_load_select == "yes":
 #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"):
 #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
-#set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
+#set singlefile_sampleName = '|'.join( [ str( $single_file.element_identifier ) for $single_file in $file_load_section.file_load_conditional.input ] )
 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
 #else
 zipfile '$file_load_section.file_load_conditional.input'
 #end if
 <option value="yes" >yes</option>
 </param>
 <when value="no">
 </when>
 <when value="yes">
-<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." />
+<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." />
 </when>
 </conditional>
 </section>
 </xml>
 </section>
 </xml>
 <!-- PEAKLIST -->
 <token name="@COMMAND_PEAKLIST@">
-#if $peaklist.peaklistBool
+#if $peaklist.peaklistBool == 'true'
 convertRTMinute $peaklist.convertRTMinute
 numDigitsMZ $peaklist.numDigitsMZ
 numDigitsRT $peaklist.numDigitsRT
 intval $peaklist.intval
 naTOzero $peaklist.naTOzero
 <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="If NA values remain, replace them by 0 in the dataMatrix" help="Mandatory for some of the downstream tools (data processing, statistics) that do not accept NA values"/>
 </xml>
 <xml name="input_peaklist_section">
 <section name="peaklist" title="Peak List" expanded="True">
-<param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" />
+<param name="peaklistBool" type="hidden" label="Get the Peak List" value="true" />
 <expand macro="input_peaklist"/>
 </section>
 </xml>
 <xml name="input_peaklist_conditional">
 <conditional name="peaklist">
-<param name="peaklistBool" type="boolean" label="Get the Peak List" />
+<param name="peaklistBool" type="select" label="Get the Peak List">
+<option value="true">Yes</option>
+<option value="false">No</option>
+</param>
 <when value="true">
 <expand macro="input_peaklist"/>
 </when>
 <when value="false" />
 </conditional>
 </xml>
 <xml name="output_peaklist"  token_function="">
 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" >
-<filter>(peaklist['peaklistBool'])</filter>
+<filter>peaklist['peaklistBool'] == 'true'</filter>
 </data>
 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" >
-<filter>(peaklist['peaklistBool'])</filter>
+<filter>peaklist['peaklistBool'] == 'true'</filter>
 </data>
 </xml>
 <token name="@HELP_PEAKLIST@">
 For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_
 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
-.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
+.. _news: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 </token>
 <token name="@HELP_XCMS_NEWVERSION_3440@">
 **Version 3.4.4.0 - 08/02/2019**
-- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
+- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS news_)
 </token>
 <token name="@HELP_XCMS_NEWVERSION_3610@">
 **Version 3.6.1+galaxy* - 03/09/2019**
-- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
+- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS news_)
 </token>
 <token name="@HELP_XCMS_NEWVERSION_31200@">
 **Version 3.12.0+galaxy* - 03/03/2020**
-- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_)
+- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS news_)
 </token>
 <xml name="citation">
 <citations>
 <citation type="doi">10.1021/ac051437y</citation>

Mercurial > repos > lecorguille > xcms_fillpeaks

comparison macros_xcms.xml @ 46:871ffc15a6da draft