diff picard_ReorderSam.xml @ 13:7e6fd3d0f16e draft

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

--- a/picard_ReorderSam.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_ReorderSam.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -6,41 +6,42 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
+    @symlink_element_identifier@
     #set $picard_dict = "localref.dict"
     #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension
-    
+
     ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
-       
+
     #if str( $reference_source.reference_source_selector ) == "history":
-        
+
       picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
       QUIET=true
       VERBOSITY=ERROR
-      
+
       &&
-      
+
     #else:
-    
+
       #set $ref_fasta = str( $reference_source.ref_file.fields.path )
-    
+
     #end if
-    
+
     picard
     ReorderSam
-      INPUT="${inputFile}"
+      INPUT='$inputFile.element_identifier'
       OUTPUT="${outFile}"
       REFERENCE="${ref_fasta}"
       ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
       ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"
-      
+
       VALIDATION_STRINGENCY="${validation_stringency}"
       QUIET=true
       VERBOSITY=ERROR
-      
+
   ]]></command>
-  
+
   <inputs>
-    
+
      <conditional name="reference_source">
       <param name="reference_source_selector" type="select" label="Load reference genome from">
         <option value="cached">Local cache</option>
@@ -55,7 +56,7 @@
           <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
         </param>
       </when>
-      <when value="history"> 
+      <when value="history">
         <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
       </when>
     </conditional>
@@ -64,7 +65,7 @@
     <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/>
     <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/>
     <expand macro="VS" />
-    
+
   </inputs>
   <outputs>
     <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
@@ -79,8 +80,8 @@
       <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 .. class:: infomark
@@ -100,14 +101,14 @@
 @description@
 
   ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean
-  S=Boolean                     If true, then allows only a partial overlap of the BAM contigs with the new reference 
-                                sequence contigs.  By default, this tool requires a corresponding contig in the new 
-                                reference for each read contig  Default value: false. Possible values: {true, false} 
-  
+  S=Boolean                     If true, then allows only a partial overlap of the BAM contigs with the new reference
+                                sequence contigs.  By default, this tool requires a corresponding contig in the new
+                                reference for each read contig  Default value: false. Possible values: {true, false}
+
   ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean
-  U=Boolean                     If true, then permits mapping from a read contig to a new reference contig with the same 
-                                name but a different length.  Highly dangerous, only use if you know what you are doing.  
-                                Default value: false.  Possible values: {true, false} 
+  U=Boolean                     If true, then permits mapping from a read contig to a new reference contig with the same
+                                name but a different length.  Highly dangerous, only use if you know what you are doing.
+                                Default value: false.  Possible values: {true, false}
 
 @more_info@
   </help>