Mercurial > repos > lecorguille > msnbase_readmsdata
diff msnbase_readmsdata.xml @ 15:7faf9b2d83f6 draft
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author | workflow4metabolomics |
---|---|
date | Mon, 11 Sep 2023 09:24:51 +0000 |
parents | 11ab2081bd4a |
children | 12def6edac2f |
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--- a/msnbase_readmsdata.xml Mon Apr 12 09:35:02 2021 +0000 +++ b/msnbase_readmsdata.xml Mon Sep 11 09:24:51 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy0"> +<tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy1"> <description>Imports mass-spectrometry data files</description> <macros> @@ -17,7 +17,7 @@ #set $source = $os.readlink(str($input)) singlefile_galaxyPath '$source' singlefile_sampleName '$os.path.basename($source)' #else - singlefile_galaxyPath '$input' singlefile_sampleName '$input.name' + singlefile_galaxyPath '$input' singlefile_sampleName '$input.element_identifier' #end if #else zipfile '$input' @@ -28,7 +28,7 @@ <inputs> - <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the following formats: mzxml, mzml, mzdata and netcdf. Zip file mode for the following formats: no_unzip.zip, zip. See the help section below." /> + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the following formats: mzxml, mzml, mzdata and netcdf. Zip file mode for the following formats: zip. See the help section below." /> </inputs> @@ -41,7 +41,7 @@ <tests> - <test> + <test expect_num_outputs="2"> <param name="input" value="faahKO_reduce.zip" ftype="zip" /> <assert_stdout> <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" /> @@ -55,7 +55,7 @@ </assert_stdout> <output name="sampleMetadata" value="sampleMetadata.tsv" /> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="ko15.CDF" ftype="netcdf" /> <assert_stdout> <has_text text="rowNames: ko15.CDF" /> @@ -123,7 +123,7 @@ ========================= ========================================== Name Format ========================= ========================================== -Upload File mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip +Upload File mzxml,mzml,mzdata,netcdf,zip ========================= ========================================== The easier way to process is to create a Dataset Collection of the type List @@ -185,14 +185,6 @@ **Step 3 : Uploading it to our Galaxy server** -If your zip file is less than 2Gb, you can use the Get Data tool to upload it. - -Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO_ on workflow4metabolomics.org. - -.. _HOWTO: http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf - -For more information, do not hesitate to send us an email at supportATworkflow4metabolomics.org. - Advices for converting your files into mzXML format (XCMS input) ----------------------------------------------------------------