Mercurial > repos > lecorguille > msnbase_readmsdata
changeset 12:d1ec753f586f draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
| author | workflow4metabolomics |
|---|---|
| date | Tue, 07 Jan 2020 09:29:47 +0000 |
| parents | 144392dd4a31 |
| children | cda005bc221c |
| files | msnbase_readmsdata.xml repository_dependencies.xml |
| diffstat | 2 files changed, 8 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/msnbase_readmsdata.xml Tue Apr 30 05:12:42 2019 -0400 +++ b/msnbase_readmsdata.xml Tue Jan 07 09:29:47 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@.1"> +<tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@.2"> <description>Imports mass-spectrometry data files</description> <macros> @@ -13,7 +13,12 @@ @COMMAND_RSCRIPT@/msnbase_readmsdata.r #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"): - singlefile_galaxyPath '$input' singlefile_sampleName '$input.name' + #if $os.path.islink(str($input)) + #set $source = $os.readlink(str($input)) + singlefile_galaxyPath '$source' singlefile_sampleName '$os.path.basename($source)' + #else + singlefile_galaxyPath '$input' singlefile_sampleName '$input.name' + #end if #else zipfile '$input' #end if @@ -107,7 +112,6 @@ ‘mzData’, ‘mzXML’ and ‘mzML’. .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html -.. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf -----------------
--- a/repository_dependencies.xml Tue Apr 30 05:12:42 2019 -0400 +++ b/repository_dependencies.xml Tue Jan 07 09:29:47 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" ?> <repositories> - <repository changeset_revision="fcc646bbf366" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/> + <repository changeset_revision="3179e95069ae" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/> <repository changeset_revision="8ce71291b600" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/> </repositories> \ No newline at end of file