diff picard_NormalizeFasta.xml @ 8:e417b1d6288d draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e

--- a/picard_NormalizeFasta.xml	Sun Nov 27 15:11:36 2016 -0500
+++ b/picard_NormalizeFasta.xml	Tue Dec 06 10:04:26 2016 -0500
@@ -6,34 +6,32 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
-    
-  
-    ## Two lines below are due to the fact that picard likes fasta files to have extension .fa  
-    #set $fasta_file="local_fasta.fa"
-    ln -s "${inputFile}" "${fasta_file}" &&    
-    
+
+    ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
+    ln -s '$inputFile' '$inputFile.element_identifier'.fa &&
+
     picard
     NormalizeFasta
-    
-    INPUT="${fasta_file}"
+
+    INPUT='$inputFile.element_identifier'.fa
     OUTPUT="${outFile}"
     LINE_LENGTH="${line_length}"
     TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
-    
+
     QUIET=true
     VERBOSITY=ERROR
-  
+
   ]]></command>
   <inputs>
     <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" />
     <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
     <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
-  </inputs> 
-  
+  </inputs>
+
   <outputs>
     <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
@@ -42,8 +40,8 @@
       <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 **Purpose**
@@ -54,10 +52,10 @@
 
 @description@
 
-  LINE_LENGTH=Integer           The line length to be used for the output fasta file.  Default value: 100. 
-  
+  LINE_LENGTH=Integer           The line length to be used for the output fasta file.  Default value: 100.
+
   TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean
-                                Truncate sequence names at first whitespace.  Default value: false. Possible values: {true, false} 
+                                Truncate sequence names at first whitespace.  Default value: false. Possible values: {true, false}
 
 @more_info@