diff macros.xml @ 16:20a75ba4345b draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907

--- a/macros.xml	Mon Jan 30 08:51:40 2017 -0500
+++ b/macros.xml	Sun Feb 05 08:57:02 2017 -0500
@@ -7,6 +7,11 @@
             <requirement type="package" version="1.1_4">r-batch</requirement>
         </requirements>
     </xml>
+    <xml name="requirements_light">
+        <requirements>
+            <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
+        </requirements>
+    </xml>
     <xml name="stdio">
         <stdio>
             <exit_code range="1" level="fatal" />
@@ -27,24 +32,40 @@
 
     <!-- zipfile load for planemo test -->
 
-    <token name="@COMMAND_ZIPFILE_LOAD@">
-        #if $zipfile_load_conditional.zipfile_load_select == "yes":
-            #if $zipfile_load_conditional.zip_file:
-                zipfile $zipfile_load_conditional.zip_file
+    <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 ] )
+
+                singlefile_galaxyPath $singlefile_galaxyPath singlefile_sampleName $singlefile_sampleName
             #end if
         #end if
     </token>
 
-    <xml name="zipfile_load">
-        <conditional name="zipfile_load_conditional">
-            <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." >
+    <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>
+                <option value="yes" >yes</option>
             </param>
             <when value="no">
             </when>
             <when value="yes">
-                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
+                <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>
@@ -54,7 +75,7 @@
     <token name="@HELP_AUTHORS@">
 .. class:: infomark
 
-**Authors**  Colin A. Smith [e-mail], Ralf Tautenhahn [e-mail], Steffen Neumann [e-mail], Paul Benton [e-mail] and Christopher Conley [e-mail] 
+**Authors**  Colin A. Smith [e-mail], Ralf Tautenhahn [e-mail], Steffen Neumann [e-mail], Paul Benton [e-mail] and Christopher Conley [e-mail]
 
 .. class:: infomark