diff macros.xml @ 6:03fdfbd914ab draft

planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce

--- a/macros.xml	Thu Sep 29 16:55:16 2016 -0400
+++ b/macros.xml	Thu Mar 30 11:27:09 2017 -0400
@@ -3,8 +3,9 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="0.4_1">r-snow</requirement>
-	        <requirement type="package" version="1.7.5">r-ipo</requirement>
-	        <requirement type="package" version="1.1_4">r-batch</requirement>
+            <requirement type="package" version="1.7.5">r-ipo</requirement>
+            <requirement type="package" version="1.1_4">r-batch</requirement>
+	    <!--<requirement type="package" version="1.7.5">r-ipo-meta</requirement>-->
         </requirements>
     </xml>
     <xml name="stdio">
@@ -14,7 +15,7 @@
     </xml>
 
     <token name="@COMMAND_SCRIPT@">
-        LANG=C Rscript $__tool_directory__/ipo.r
+        LANG=C Rscript $__tool_directory__/
     </token>
 
     <token name="@COMMAND_LOG_EXIT@">
@@ -25,10 +26,54 @@
         sh -c "exit \$return"
     </token>
 
+    <token name="@COMMAND_NSLAVES@">
+        nSlaves \${GALAXY_SLOTS:-1}
+    </token>
+
+    <!-- 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 ] )
+
+                singlefile_galaxyPath $singlefile_galaxyPath singlefile_sampleName $singlefile_sampleName
+            #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>
+
     <token name="@HELP_AUTHORS@">
 .. class:: infomark
 
-**Authors**  Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber and Christoph Magnes 
+**Authors**  Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber and Christoph Magnes
 
 .. class:: infomark