Mercurial > repos > workflow4metabolomics > xcms_refine
diff macros_xcms.xml @ 1:20f8ebc3a391 draft
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author | workflow4metabolomics |
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date | Mon, 11 Sep 2023 09:19:47 +0000 |
parents | eb115eb8f25c |
children |
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--- a/macros_xcms.xml Thu Jun 17 07:42:55 2021 +0000 +++ b/macros_xcms.xml Mon Sep 11 09:19:47 2023 +0000 @@ -2,6 +2,8 @@ <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> @@ -17,7 +19,7 @@ #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 @@ -36,7 +38,7 @@ <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> @@ -80,7 +82,7 @@ <!-- PEAKLIST --> <token name="@COMMAND_PEAKLIST@"> - #if $peaklist.peaklistBool + #if $peaklist.peaklistBool == 'true' convertRTMinute $peaklist.convertRTMinute numDigitsMZ $peaklist.numDigitsMZ numDigitsRT $peaklist.numDigitsRT @@ -103,14 +105,17 @@ <xml name="input_peaklist_section"> <section name="peaklist" title="Peak List" expanded="True"> - <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" /> + <param name="peaklistBool" type="hidden" label="Get the Peak List" value="true" /> <expand macro="input_peaklist"/> </section> </xml> <xml name="input_peaklist_conditional"> <conditional name="peaklist"> - <param name="peaklistBool" type="boolean" label="Get the Peak List" /> + <param name="peaklistBool" type="select" label="Get the Peak List"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> <when value="true"> <expand macro="input_peaklist"/> </when> @@ -120,10 +125,10 @@ <xml name="output_peaklist" token_function=""> <data name="variableMetadata" format="tabular" label="${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> @@ -243,24 +248,24 @@ .. _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">