diff macros.xml @ 22:411d2b9ea412 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d

--- a/macros.xml	Fri Feb 10 11:02:38 2017 -0500
+++ b/macros.xml	Wed Mar 01 16:57:27 2017 -0500
@@ -33,41 +33,50 @@
     <!-- zipfile load for planemo test -->
 
     <token name="@COMMAND_FILE_LOAD@">
-        #if $file_load_conditional.file_load_select == "yes":
-            #if $file_load_conditional.inputs.input == "zip_file":
-                zipfile '$file_load_conditional.inputs.zip_file'
-            #else
-                #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] )
-                #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] )
+        #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 ] )
 
                 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
+            #else
+                zipfile '$file_load_section.file_load_conditional.input'
             #end if
         #end if
     </token>
 
-    <xml name="file_load">
-        <conditional name="file_load_conditional">
-            <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
-                <option value="no" >no need</option>
-                <option value="yes" >yes</option>
-            </param>
-            <when value="no">
-            </when>
-            <when value="yes">
-                <conditional name="inputs">
-                    <param name="input" type="select" label="Choose your inputs method" >
-                        <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
-                        <option value="single_file">A mzXML or netCDF file from your history</option>
-                    </param>
-                    <when value="zip_file">
-                        <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
-                    </when>
-                    <when value="single_file">
-                        <param name="single_file" type="data" format="mzxml,netcdf" label="Single file"  multiple="true"/>
-                    </when>
-                </conditional>
-            </when>
-        </conditional>
+    <xml name="input_file_load">
+        <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
+                    <option value="no" >no need</option>
+                    <option value="yes" >yes</option>
+                </param>
+                <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." />
+                </when>
+            </conditional>
+        </section>
+    </xml>
+
+    <xml name="test_file_load_zip">
+        <section name="file_load_section">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes" />
+                <param name="input" value="faahKO_reduce.zip" ftype="zip" />
+            </conditional>
+        </section>
+    </xml>
+
+    <xml name="test_file_load_single">
+        <section name="file_load_section">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes" />
+                <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
+            </conditional>
+        </section>
     </xml>
 
     <token name="@COMMAND_PEAKLIST@">