--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_CollectSequencingArtifactsMetrics.xml	Thu May 16 07:13:32 2019 -0400
@@ -0,0 +1,148 @@
+<tool id='picard_artifact_metrics' name='Picard Collect Sequencing Artifact Metrics' version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+  <description>Collect metrics to quantify single-base sequencing artifacts</description>
+  <macros>
+    <import>picard_macros.xml</import>
+    <token name="@WRAPPER_VERSION@">1</token>
+  </macros>
+  <expand macro="requirements">
+    <requirement type="package" version="3.4.1">r-base</requirement>
+  </expand>
+  <command detect_errors="exit_code"><![CDATA[
+    @java_options@
+    @symlink_element_identifier@
+    
+    #set $reference_fasta_filename = "localref.fa"
+    @handle_reference_source@
+    
+    picard 
+    CollectSequencingArtifactMetrics 
+    I='$escaped_element_identifier'
+    O='OutPut'
+    R='${reference_fasta_filename}'
+    AS=${assume_sorted}
+    CONTEXT_SIZE=${context_size}
+    INCLUDE_DUPLICATES='${duplicates}'
+    #if $contexts_to_print 
+      #for $context in str($contexts_to_print).split(','):
+          CONTEXTS_TO_PRINT='${context}'
+      #end for;
+    #end if;
+    MINIMUM_QUALITY_SCORE='${min_quality_score}'
+    INCLUDE_UNPAIRED='${unpaired}'
+    MAXIMUM_INSERT_SIZE='${max_size}'
+    MINIMUM_INSERT_SIZE='${min_size}'
+    MINIMUM_MAPPING_QUALITY='${minim_map_quality}';
+  ]]></command>  
+  <inputs>
+    <param name='inputFile' format="sam,bam" type='data' label='SAM/BAM Input file'/>
+    <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="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="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='context_size' value="1" type='integer' label='How many nucleotides (context) on each side to consider' help='e.g NXN corresponds to 1 "N" on each side of "X"'/>
+    <param name="contexts_to_print" type="text" label="Contexts to print in the detailed tables, separated by comma (avoid spaces)" help="e.g. (for context size=1) AAA,AGG. Default prints all contexts">
+        <sanitizer>
+            <valid initial="string.letters"><add value="," /></valid>
+        </sanitizer>
+    </param>  
+    <param name='min_quality_score' type='integer' value='30' label='Minimum base quality score'/>
+    <param name="max_size" type="integer" value="600" label="Maximum insert size"/>
+    <param name="min_size" type="integer" value="30" label="Minimum insert size"/>
+    <param name="minim_map_quality" type="integer" value="20" label="Minimum mapping quality"/>
+    <param name='assume_sorted' type='boolean' label='Assume SAM/BAM is sorted'/>
+    <param name='duplicates' type='boolean' label='Include duplicates' checked="false" truevalue="true" falsevalue="false"/>
+    <param name='unpaired' type='boolean' label='Include unpaired reads' checked="false" truevalue="true" falsevalue="false"/>
+
+    <expand macro="VS" />
+
+  </inputs>
+
+  <outputs>
+    <data name='pre_details' format="tabular"  from_work_dir="OutPut.pre_adapter_detail_metrics" label='Detailed table for artifacts introduced prior to the addition of adapters'/>
+    <data name='pre_summary' format="tabular"  from_work_dir="OutPut.pre_adapter_summary_metrics" label='Summary table for artifacts introduced prior to the addition of adapters'/>
+    <data name='pos_details' format="tabular"  from_work_dir="OutPut.bait_bias_detail_metrics" label='Detailed table for artifacts introduced posterior to the addition of adapters'/>
+    <data name='pos_summary' format="tabular"  from_work_dir="OutPut.bait_bias_summary_metrics" label='Summary table for artifacts introduced posterior to the addition of adapters'/>
+    <data name='err_summary' format="tabular"  from_work_dir="OutPut.error_summary_metrics" label='General Summary of artifactual errors'/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" />
+      <param name="reference_source_selector" value="history"/>
+      <param name="ref_file" value="picard_BedToIntervalList_ref.fa" />
+      <param name="context_size" value="1" />
+      <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />
+      <output name='pre_details' file='pre_details' ftype="tabular"  value="pre_detail" lines_diff="4"/>
+      <output name='pre_summary' file='pre_summary' ftype="tabular"  value="pre_summary" lines_diff="4"/>
+      <output name='pos_details' file='pos_details' ftype="tabular"  value="pos_detail" lines_diff="4"/>
+      <output name='pos_summary' file='pos_summary' ftype="tabular"  value="pos_summary" lines_diff="4"/>
+      <output name='err_summary' file='err_summary' ftype="tabular"  value="err_summary" lines_diff="4"/>
+    </test>
+    <test>
+      <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/>
+      <param name="reference_source_selector" value="cached"/>
+      <param name="context_size" value="1" />
+      <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />
+      <output name='pre_details' file='pre_details' ftype="tabular"  value="pre_detail" lines_diff="4"/>
+      <output name='pre_summary' file='pre_summary' ftype="tabular"  value="pre_summary" lines_diff="4"/>
+      <output name='pos_details' file='pos_details' ftype="tabular"  value="pos_detail" lines_diff="4"/>
+      <output name='pos_summary' file='pos_summary' ftype="tabular"  value="pos_summary" lines_diff="4"/>
+      <output name='err_summary' file='err_summary' ftype="tabular"  value="err_summary" lines_diff="4"/>
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Program to chart the distribution of potential sequencing "single nucleotide mutation" artifacts in a SAM or BAM file.
+
+@dataset_collections@
+
+@description@
+
+  ASSUME_SORTED=Boolean           If true (default), then the sort order in the header file will be ignored.  
+                                  Default: True
+
+  CONTEXT_SIZE=integer            The number of context bases to include on each side of the assayed base.
+  
+  CONTEXT_SIZE_TO_PRINT=String    If specified, only print results for these contexts in the detail metrics output. 
+                                  However, the summary metrics output will still take all contexts into consideration.
+                                
+  DB_SNP=text file                VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.
+
+  INCLUDE_DUPLICATES=Boolean      Include duplicate reads. If set to true then all reads flagged as duplicates will be included as well.
+
+  INCLUDE_UNPAIRED=Boolean        Include unpaired reads. If set to true then all paired reads will be included as well - 
+                                  MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored.
+
+  MAXIMUM_INSERT_SIZE=Integer     The maximum insert size for a read to be included in analysis. Set to 0 to have no maximum.
+                                  Default = 600
+
+  MINIMUM_INSERT_SIZE=Integer     The minimum insert size for a read to be included in analysis. Default = 60
+
+  MINIMUM_MAPPING_QUALITY         The minimum mapping quality score for a base to be included in analysis. Default = 30
+
+  MINIMUM_QUALITY_SCORE           The minimum base quality score for a base to be included in analysis. Default = 20
+
+@more_info@
+
+  </help>
+  <expand macro="citations" />
+</tool>