Test data change to lighter files

Removing former test data to use lighter files (~3Mb each) and implementing suitable changes into .xml and readme

tools/mzxmlshaper/README.md

@@ -35,14 +35,13 @@ Configuration
 Technical description
 -----------
 
-Main files:
+Main files: ## à modifier
 
 - mzXMLShaper.R: R function (core script)
 - mzXMLShaper.xml: XML wrapper (interface for Galaxy)
-- 111-1_POS01.CDF (test file): Riker Metabolome Database (http://metabobank.riken.jp/metabo/db/plantMetabolomics/http:/metadb.riken.jp/db/plantMetabolomics/0.1/File/RPMM0054_111-1)
-- BlancFin_POS_RA1_1_6869.mzML (test file): Internal blank sample, PFEM - INRAE (https://pfem.isc.inrae.fr/)
-- example.mzXML (test file): PRIDE Toolsuite (https://github.com/PRIDE-Toolsuite/inspector-example-files/blob/master/peak-files/example.mzXML.gz)
-
+- ko16.CDF: netCDF test file from faahKO Bioconductor package (https://www.bioconductor.org/packages/release/data/experiment/html/faahKO.html)
+- ko16.mzml: ko.CDF file converted to mzML using mzR R package
+- ko16.mzXml: ko.CDF file converted to mzXML using mzR R package
 
 Services provided
 -----------

tools/mzxmlshaper/mzXMLShaper.xml

@@ -15,6 +15,7 @@
       #if str($outformat) == 'mzml':
         outputfilename '$mzml_file'
       #elif str($outformat) == 'mzXml':
+        str($outformat) == 'mzXml':
         outputfilename '$mzXml_file'
       #end if
   ]]></command>
@@ -29,38 +30,38 @@
     <data format="mzml" label="${infile.name}_converted.mzml" name="mzml_file">
       <filter>outformat=="mzml"</filter>
     </data>
-    <data format="mzxml" label="${infile.name}_converted.mzxml" name="mzXml_file">
+    <data format="mzxml" label="${infile.name}_converted.mzml" name="mzXml_file">
       <filter>outformat=="mzXml"</filter>
     </data>
   </outputs>
   <tests>
     <test expect_num_outputs="1">
-      <param name="infile" value="original_data/111-1_POS01.CDF"/>
+      <param name="infile" value="original_data/ko16.CDF"/>
       <param name="outformat" value="mzml"/>
-      <output name="mzml_file" file="conversion_result_cdf_to_mzml.mzml"/>
+      <output name="mzml_file" file="conversion_result_cdf_to_mzml.mzml" />
     </test>
     <test expect_num_outputs="1">
-      <param name="infile" value="original_data/111-1_POS01.CDF"/>
+      <param name="infile" value="original_data/ko16.CDF"/>
       <param name="outformat" value="mzXml"/>
       <output name="mzXml_file" file="conversion_result_cdf_to_mzxml.mzxml"/>
     </test>
     <test expect_num_outputs="1">
-      <param name="infile" value="original_data/example.mzXML"/>
+      <param name="infile" value="original_data/ko16.mzXml"/>
       <param name="outformat" value="mzml"/>
-      <output name="mzml_file" file="conversion_result_mzxml_to_mzml.mzml"/>
+      <output name="mzml_file" file="conversion_result_mzxml_to_mzml.mzml" />
     </test>
     <test expect_num_outputs="1">
-      <param name="infile" value="original_data/example.mzXML"/>
+      <param name="infile" value="original_data/ko16.mzXml"/>
       <param name="outformat" value="mzXml"/>
       <output name="mzXml_file" file="conversion_result_mzxml_to_mzxml.mzxml"/>
     </test>
     <test expect_num_outputs="1">
-      <param name="infile" value="original_data/BlancFin_POS_RA1_1_6869.mzML"/>
+      <param name="infile" value="original_data/ko16.mzml"/>
       <param name="outformat" value="mzml"/>
-      <output name="mzml_file" file="conversion_result_mzml_to_mzml.mzml"/>
+      <output name="mzml_file" file="conversion_result_mzml_to_mzml.mzml" />
     </test>
     <test expect_num_outputs="1">
-      <param name="infile" value="original_data/BlancFin_POS_RA1_1_6869.mzML"/>
+      <param name="infile" value="original_data/ko16.mzml"/>
       <param name="outformat" value="mzXml"/>
       <output name="mzXml_file" file="conversion_result_mzml_to_mzxml.mzxml"/>
     </test>