changeset 143:b2ca2d181fb4 draft

fixed downsample sam in picard1106 (accept bam)

--- a/picard_DownsampleSam.xml	Thu Feb 27 13:15:52 2014 -0500
+++ b/picard_DownsampleSam.xml	Mon Jun 16 17:38:15 2014 -0400
@@ -1,30 +1,37 @@
-<tool name="Downsample SAM" id="picard_DownsampleSam" version="1.106.0">
+<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="1.106.0">
     <!-- found on https://bitbucket.org/bwlang/galaxy-dist/src/ca5ded2e18a9ef802c31429e3cb861e8775b24d0/tools/picard/picard_DownsampleSam.xml -->
    <description>Down-sample a file to retain a subset of the reads</description>
    <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
-      --input=$inputFile
-      --output=$outFile
+      --input "$inputFile"
+      --output "$outFile"
       --probability=$probability
+      --output-format $outputFormat
       --seed=$seed
       -j "\$JAVA_JAR_PATH/DownsampleSam.jar"
   </command>
   <inputs>
-    <param format="sam" name="inputFile" type="data" label="SAM dataset to be downsampled"
-           help="If empty, upload or import a SAM dataset." />
+    <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset to be downsampled"
+           help="If empty, upload or import a SAM or BAM dataset." />
     <param name="probability" type="float" size="5" label="Probability (between 0 and 1) that any given read will be kept" help="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="(same seed + same probability = same set of reads kept)" value="1" />
+    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
   </inputs>
   <outputs>
-    <data name="outFile" format="sam" label="${tool.name} on ${on_string}">
+    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled ${outputFormat}">
+      <change_format>
+        <when input="outputFormat" value="sam" format="sam" />
+      </change_format>
     </data>
   </outputs>
+ 
   <tests>
     <test>
-      <param name="inputFile" value="cleansamtestinput.sam" />
+      <param name="inputFile" value="cleansamtestinput.sam"  ftype="sam" />
       <param name="probability" value="0.1" />
       <param name="seed" value="2" />
+      <param name="outputFormat" value="False" />
       <output name="outFile" file="downsamplesamoutput.sam" ftype="sam" />
     </test>
   </tests>
@@ -54,4 +61,4 @@
 
 
   </help>
-</tool>
\ No newline at end of file
+</tool>

--- a/picard_wrapper.py	Thu Feb 27 13:15:52 2014 -0500
+++ b/picard_wrapper.py	Mon Jun 16 17:38:15 2014 -0400
@@ -800,18 +800,21 @@
         cl.append('OUTPUT=%s' % tempout)
         pic.runPic(opts.jar, cl)
         haveTempout = True
+
     elif pic.picname == "DownsampleSam":
         cl.append('I=%s' % opts.input)
-        mystring = opts.output
-        mystringsam = mystring + ".sam"
-        cl.append('O=%s' % mystringsam)
+        output_string = opts.output
+        if opts.datatype == 'sam':
+            output_string = output_string + ".sam"
+        cl.append('O=%s' % output_string)
         if float(opts.probability) > 0:
             cl.append('PROBABILITY=%s' % opts.probability)
         if float(opts.seed) > 0:
             cl.append('RANDOM_SEED=%s' % opts.seed)
         stdouts,rval = pic.runPic(opts.jar, cl)
-        myoutput = mystringsam.replace(".sam", "")
-        os.rename(mystringsam,myoutput)
+        if opts.input.endswith(".sam"):
+            renamed_output = output_string.replace(".sam", "")
+            os.rename(output_string,renamed_output)
 
     elif pic.picname == 'MeanQualityByCycle':
         isPDF = 'MeanQualityByCycle.pdf'