diff picard_CollectWgsMetrics.xml @ 3:52fdfc45590a draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_CollectWgsMetrics.xml	Thu Jul 16 15:32:31 2015 -0400
@@ -0,0 +1,107 @@
+<tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.0">
+  <description>compute metrics for evaluating of whole genome sequencing experiments</description>
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <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( $reference_source.ref_file.fields.path )
+    #end if
+    
+    java -jar \$JAVA_JAR_PATH/picard.jar
+    CollectWgsMetrics
+    INPUT="${inputFile}"
+    OUTPUT="${outFile}"
+    REFERENCE_SEQUENCE="${reference_fasta_filename}"
+    MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}"
+    MINIMUM_BASE_QUALITY="${minimum_base_quality}"
+    COVERAGE_CAP="${coverage_cap}"
+    
+    VALIDATION_STRINGENCY="${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="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for a read to contribute coverage" help="MINIMUM_MAPPING_QUALITY; default=20"/>
+    <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20"/>
+    <param name="coverage_cap" type="integer" value="250" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=250"/>
+
+    
+    <expand macro="VS" />
+    
+  </inputs>
+  
+  <outputs>
+    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="reference_source_selector" value="history" />
+      <param name="minimum_mapping_quality" value="20" />
+      <param name="minimum_base_quality" value="20" />
+      <param name="coverage_cap" value="250" />
+      <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" />
+      <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" />
+      <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
+    </test> 
+  </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
+
+@dataset_collections@
+
+@description@
+
+  MINIMUM_MAPPING_QUALITY=Integer
+  MQ=Integer                    Minimum mapping quality for a read to contribute coverage.  Default value: 20. 
+
+  MINIMUM_BASE_QUALITY=Integer
+  Q=Integer                     Minimum base quality for a base to contribute coverage.  Default value: 20. 
+
+  COVERAGE_CAP=Integer
+  CAP=Integer                   Treat bases with coverage exceeding this value as if they had coverage at this value.  
+                                Default value: 250. 
+
+@more_info@
+
+  </help>
+</tool>
+
+