--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_CollectAlignmentSummaryMetrics.xml	Tue Dec 16 19:03:21 2014 -0500
@@ -0,0 +1,137 @@
+<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="1.126.0">
+  <description>writes a file containing summary alignment metrics</description>
+  <requirements>
+    <requirement type="package" version="1.126.0">picard</requirement>
+  </requirements>
+  
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  
+  <command>
+    @java_options@
+    ##set up input files
+
+    #set $reference_fasta_filename = "localref.fa"
+    
+    #if str( $reference_source.reference_source_selector ) == "history":
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+    #else:
+        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+    #end if
+    
+    java -jar \$JAVA_JAR_PATH/picard.jar
+    CollectAlignmentSummaryMetrics
+    INPUT="${inputFile}"
+    OUTPUT="${outFile}"
+    MAX_INSERT_SIZE=${maxinsert}
+    #for $sequence in $adapters:
+        ADAPTER_SEQUENCE="${sequence.adapter}"
+    #end for
+    METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
+    IS_BISULFITE_SEQUENCED="${bisulphite}"
+    
+    REFERENCE_SEQUENCE="${reference_fasta_filename}"
+    
+    ASSUME_SORTED="${assume_sorted}"
+
+    VALIDATION_STRINGENCY="${validation_stringency}"
+    QUIET=true
+    VERBOSITY=ERROR
+  
+  </command>
+  <inputs>
+    <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."/>
+    <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="cached">
+        <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
+          <options from_data_table="all_fasta">
+          </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
+      </when>
+    </conditional>
+    <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
+      <option value="ALL_READS" selected="True">All reads</option>
+      <option value="SAMPLE">Sample</option>
+      <option value="LIBRARY">Library</option>
+      <option value="READ_GROUP">Read group</option>
+    </param>
+    <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
+    <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/>
+    <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences">
+          <param name="adapter" type="text" size="50" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
+    </repeat>
+    <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" size="20" help="MAX_INSERT_SIZE"/>
+    
+    <expand macro="VS" />
+    
+  </inputs>
+  
+  <outputs>
+    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
+  </outputs>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  
+  <tests>
+    <test>
+      <param name="bisulphite" value="false" />
+      <param name="sorted" value="true" />
+      <param name="adaptors" value="" />
+      <param name="maxinsert" value="100000" />
+      <param name="reference_source_selector" value="history" />
+      <param name="ref_file" value="picard_CASM_ref.fa" />
+      <param name="inputFile" value="picard_CASM.bam" ftype="bam" />
+      <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
+    </test>
+  </tests>
+  
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Reads a SAM or BAM file and writes a file containing summary alignment metrics.
+
+@dataset_collections@
+
+@description@
+
+  MAX_INSERT_SIZE=Integer       Paired end reads above this insert size will be considered chimeric along with 
+                                inter-chromosomal pairs.  Default value: 100000.  
+
+  ADAPTER_SEQUENCE=String       List of adapter sequences to use when processing the alignment metrics  This option may 
+                                be specified 0 or more times.  
+
+  METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
+  LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics.    Possible values: {ALL_READS, SAMPLE, 
+                                LIBRARY, READ_GROUP} This option may be specified 0 or more times.  
+
+  IS_BISULFITE_SEQUENCED=Boolean
+  BS=Boolean                    Whether the SAM or BAM file consists of bisulfite sequenced reads.    
+
+
+  REFERENCE_SEQUENCE=File
+  R=File                        Reference sequence fasta  Default value: null. 
+
+  ASSUME_SORTED=Boolean
+  AS=Boolean                    If true (default), then the sort order in the header file will be ignored. 
+
+@more_info@
+
+  </help>
+</tool>
+
+