diff macros.xml @ 25:230f0bc9e792 draft

planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa

--- a/macros.xml	Wed Feb 01 12:23:07 2017 -0500
+++ b/macros.xml	Fri Feb 10 11:11:27 2017 -0500
@@ -19,33 +19,68 @@
     <token name="@COMMAND_CAMERA_SCRIPT@">
         LANG=C Rscript $__tool_directory__/CAMERA.r
     </token>
-    
+
     <!-- 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    
+        #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" selected="peakgroups">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>
-    
+
+    <token name="@COMMAND_PEAKLIST@">
+        convertRTMinute $convertRTMinute
+        numDigitsMZ $numDigitsMZ
+        numDigitsRT $numDigitsRT
+        intval $intval
+    </token>
+
+    <xml name="input_peaklist">
+        <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
+        <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
+        <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
+        <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
+            <option value="into" selected="true">into</option>
+            <option value="maxo" >maxo</option>
+            <option value="intb">intb</option>
+        </param>
+    </xml>
+
     <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