diff picard_DownsampleSam.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_DownsampleSam.xml	Thu Jul 16 15:32:31 2015 -0400
@@ -0,0 +1,75 @@
+<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.0">
+  <description>Downsample a file to retain a subset of the reads</description>
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>
+    @java_options@
+    java -jar
+    \$JAVA_JAR_PATH/picard.jar
+    DownsampleSam
+      INPUT="${inputFile}"
+      OUTPUT="${outFile}"
+      PROBABILITY=${probability}
+      RANDOM_SEED=${seed}
+      QUIET=true
+      VERBOSITY=ERROR
+      VALIDATION_STRINGENCY=${validation_stringency}
+  </command>
+  <inputs>
+    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" />
+    <param name="probability" type="float" size="4" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
+    <param name="seed" type="integer" size="5" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
+    
+    <expand macro="VS" />
+    
+  </inputs>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <outputs>
+    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="inputFile" value="picard_DownsampleSam.bam"  ftype="bam" />
+      <param name="probability" value="0.1" />
+      <param name="seed" value="1024" />
+      <param name="validation_stringency" value="LENIENT" />
+      <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam"/>
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Randomly down-sample a SAM or BAM file to retain a random subset of the reads. Mate-pairs are either both kept or both discarded. Reads marked as not primary alignments are all discarded. Each read is given a probability P of being retained - results with the exact same input in the same order and with the same value for RANDOM_SEED will produce the same results.
+
+@dataset_collections@
+
+@description@
+
+  INPUT=File
+  I=File              The input SAM or BAM file to downsample.  Required. 
+
+  OUTPUT=File
+  O=File              The output, downsampled, SAM or BAM file to write.  Required. 
+
+  RANDOM_SEED=Long
+  R=Long              Random seed to use if reproducibilty is desired.  Setting to null will cause multiple
+                      invocations to produce different results.
+                      
+  PROBABILITY=Double
+  P=Double            The probability of keeping any individual read, between 0 and 1. 
+                       
+
+
+@more_info@
+  </help>
+</tool>