diff msnbase_readmsdata.xml @ 15:b25a582ab6c1 draft

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

--- a/msnbase_readmsdata.xml	Mon Apr 12 09:34:31 2021 +0000
+++ b/msnbase_readmsdata.xml	Mon Jul 15 15:56:53 2024 +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@+galaxy2">
     <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'
@@ -28,20 +28,17 @@
 
     <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>
 
     <outputs>
         <data name="xsetRData" format="rdata.msnbase.raw" label="${input.name.rsplit('.',1)[0]}.raw.RData" from_work_dir="readmsdata.RData" />
-        <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv" >
-            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
-        </data>
     </outputs>
 
     <tests>
 
-        <test>
+        <test expect_num_outputs="1">
             <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" />
@@ -53,9 +50,8 @@
                 <has_text text="faahKO_reduce/WT/wt15.CDF        wt15           WT" />
                 <has_text text="faahKO_reduce/WT/wt16.CDF        wt16           WT" />
             </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 +119,7 @@
 ========================= ==========================================
 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 +181,6 @@
 
 **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)
 ----------------------------------------------------------------