--- a/picard_ReorderSam.xml	Fri Feb 21 12:07:49 2014 -0500
+++ b/picard_ReorderSam.xml	Tue Dec 16 19:03:21 2014 -0500
@@ -1,155 +1,120 @@
-<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0">
-  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
-  <command interpreter="python">
-    picard_wrapper.py
-      --input="${inputFile}"
-      #if $source.indexSource == "built-in"
-        --ref="${source.ref.fields.path}"
-      #else
-        --ref-file="${refFile}"
-        --species-name="${source.speciesName}"
-        --build-name="${source.buildName}"
-        --trunc-names="${source.truncateSeqNames}"
-      #end if
-      --allow-inc-dict-concord="${allowIncDictConcord}"
-      --allow-contig-len-discord="${allowContigLenDiscord}"
-      --output-format="${outputFormat}"
-      --output="${outFile}"
-      --tmpdir "${__new_file_path__}" 
-      -j "\$JAVA_JAR_PATH/ReorderSam.jar"
+<tool name="ReorderSam" id="picard_ReorderSam" version="1.126.0">
+  <description>reorder reads to match ordering in reference sequences</description>
+  <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements>
+  
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  
+  <command>
+    @java_options@
+    #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}" &amp;&amp;
+       
+    #if str( $reference_source.reference_source_selector ) == "history":
+        
+      java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
+      QUIET=true
+      VERBOSITY=ERROR
+      
+      &amp;&amp;
+      
+    #else:
+    
+      #set $ref_fasta = str( $reference_source.ref_file.fields.path )
+    
+    #end if
+    
+    java -jar \$JAVA_JAR_PATH/picard.jar
+    ReorderSam
+      INPUT="${inputFile}"
+      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>
-    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"
-           help="If empty, upload or import a SAM/BAM dataset." />
-    <conditional name="source">
-      <param name="indexSource" type="select" label="Select Reference Genome" help="This tool will re-order SAM/BAM in the same order as reference selected below.">
-        <option value="built-in">Locally cached</option>
+    
+     <conditional name="reference_source">
+      <param name="reference_source_selector" type="select" label="Load reference genome from">
+        <option value="cached">Local cache</option>
         <option value="history">History</option>
       </param>
-      <when value="built-in">
-        <param name="ref" type="select" label="Select a reference genome">
-          <options from_data_table="picard_indexes" />
+      <when value="cached">
+        <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
+          <options from_data_table="picard_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+          <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">
-        <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
-        <param name="speciesName" type="text" value="" label="Species name" />
-        <param name="buildName" type="text" value="" label="Build name" />
-        <param name="truncateSeqNames" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Truncate sequence names after first whitespace" />
+      <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>
-    <param name="allowIncDictConcord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow incomplete dict concordance?" help="Allows a partial overlap of the BAM contigs with the new reference sequence contigs." />
-    <param name="allowContigLenDiscord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow contig length discordance?" help="This is dangerous--don't check it unless you know exactly what you're doing!" />
-    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
+
+    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+    <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 ${outputFormat}">
-      <change_format>
-        <when input="outputFormat" value="sam" format="sam" />
-      </change_format>
-    </data>
+    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
   </outputs>
   <tests>
     <test>
-      <!-- Commands:
-      cp test-data/phiX.fasta .
-      samtools faidx phiX.fasta
-      java -jar CreateSequenceDictionary.jar R=phiX.fasta O=phiX.dict URI=phiX.fasta TRUNCATE_NAMES_AT_WHITESPACE=false SPECIES=phiX174
-      java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input1.bam O=picard_RS_output1.bam REFERENCE=phiX.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
-    -->
-      <param name="inputFile" value="picard_RS_input1.bam" />
-      <param name="indexSource" value="history" />
-      <param name="refFile" value="phiX.fasta" />
-      <param name="speciesName" value="phiX174" />
-      <param name="buildName" value="" />
-      <param name="truncateSeqNames" value="false" />
-      <param name="allowIncDictConcord" value="false" />
-      <param name="allowContigLenDiscord" value="false" />
-      <param name="outputFormat" value="True" />
-      <output name="outFile" file="picard_RS_output1.bam" ftype="bam" lines_diff="4" compare="contains" />
-    </test>
-    <test>
-      <!-- Command:
-      java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input2.sam O=picard_RS_output2.sam REFERENCE=/path/to/phiX/picard_index/phiX.fa ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
-      /path/to/phiX/srma_index/phiX.fa is path to phiX.fa, phiX.fa.fai, and phiX.dict
-      -->
-      <param name="inputFile" value="picard_RS_input2.sam" />
-      <param name="indexSource" value="built-in" />
-      <param name="ref" value="phiX" />
-      <param name="allowIncDictConcord" value="false" />
-      <param name="allowContigLenDiscord" value="false" />
-      <param name="outputFormat" value="False" />
-      <output name="outFile" file="picard_RS_output2.sam" ftype="sam" lines_diff="4" sort="True" />
-    </test>
-    <test>
-      <!-- Commands:
-      cp test-data/picard_RS_input4.fasta .
-      samtools faidx picard_RS_input4.fasta
-      java -jar CreateSequenceDictionary.jar R=picard_RS_input4.fasta O=picard_RS_input4.dict URI=picard_RS_input4.fasta TRUNCATE_NAMES_AT_WHITESPACE=true SPECIES=phiX174 GENOME_ASSEMBLY=phiX_buildBlah1.1
-      java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input3.bam O=picard_RS_output3.sam REFERENCE=picard_RS_input4.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false
-      picard_RS_input3.bam can be made from picard_RS_input3.sam
-      -->
-      <param name="inputFile" value="picard_RS_input3.bam" />
-      <param name="indexSource" value="history" />
-      <param name="refFile" value="picard_RS_input4.fasta" />
-      <param name="speciesName" value="phiX174" />
-      <param name="buildName" value="phiX_buildBlah1.1" />
-      <param name="truncateSeqNames" value="true" />
-      <param name="allowIncDictConcord" value="true" />
-      <param name="allowContigLenDiscord" value="false" />
-      <param name="outputFormat" value="False" />
-      <output name="outFile" file="picard_RS_output3.sam" ftype="sam" lines_diff="12" sort="True" />
+      <param name="reference_source_selector" value="history" />
+      <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" />
+      <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
+      <param name="allow_incomplete_dict_concordance" value="false"/>
+      <param name="allow_contig_length_discordance" value="false"/>
+      <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="2"/>
     </test>
   </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
   <help>
 
 .. class:: infomark
 
 **Purpose**
 
-Reorder SAM/BAM to match contig ordering in a particular reference file. Note that this is
-not the same as sorting as done by the SortSam tool, which sorts by either coordinate
-values or query name. The ordering in ReorderSam is based on exact name matching of
-contigs/chromosomes. Reads that are mapped to a contig that is not in the new reference file are
-not included in the output.
-
-**Picard documentation**
-
-This is a Galaxy wrapper for ReorderSam, a part of the external package Picard-tools_.
-
- .. _Picard-tools: http://www.google.com/search?q=picard+samtools
-
-------
-
-.. class:: infomark 
+ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs.  Reads mapped to contigs absent in the new reference are dropped.
 
-**Inputs, outputs, and parameters**
-
-For the file that needs to be reordered, either a sam file or a bam file must be supplied.
-If a bam file is used, it must be coordinate-sorted. A reference file is also required,
-so either a fasta file should be supplied or a built-in reference can be selected.
+@dataset_collections@
 
-The output contains the same reads as the input file but the reads have been rearranged so
-they appear in the same order as the provided reference file. The tool will output either
-bam (the default) or sam, according to user selection. Bam is recommended since it is smaller.
-
-The only extra parameters that can be set are flags for allowing incomplete dict concordance
-and allowing contig length discordance. If incomplete dict concordance is allowed, only a
-partial overlap of the bam contigs with the new reference sequence contigs is required. By
-default it is off, requiring a corresponding contig in the new reference for each read contig.
-If contig length discordance is allowed, contig names that are the same between a read and the
-new reference contig are allowed even if they have different lengths. This is usually not a
-good idea, unless you know exactly what you're doing. It's off by default.
+----
 
 .. class:: warningmark
 
-**Warning on SAM/BAM quality**
+Not to be confused with **SortSam**.
+
+@description@
 
-Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
-flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
-to be the only way to deal with SAM/BAM that cannot be parsed.
+  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} 
+  
+  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} 
 
-
+@more_info@
   </help>
 </tool>
 
@@ -164,3 +129,4 @@
 
 
 
+