diff correctGCBias.xml @ 16:d9a0a017896a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/correctGCBias.xml	Sat Feb 15 15:41:04 2014 -0500
@@ -0,0 +1,109 @@
+<tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.4">
+    <description>uses the output from computeGCBias to generate corrected BAM files</description>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@BINARY@">correctGCBias</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <command>
+        #import tempfile
+        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+
+        #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
+        #set $temp_bam_path = $temp_bam_handle.name + '.bam'
+        #silent $temp_bam_handle.close()
+        #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
+        #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))
+
+
+        correctGCBias
+
+        @THREADS@
+
+        --bamfile '$temp_bam_path'
+        --GCbiasFrequenciesFile $GCbiasFrequenciesFile
+
+        @reference_genome_source@
+
+
+        #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
+            --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
+        #else:
+            --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
+        #end if
+
+        #if str($region).strip() != '':
+            --region '$region'
+        #end if
+
+        #if $advancedOpt.showAdvancedOpt == "yes":
+            --binSize '$advancedOpt.binSize'  
+        #end if
+
+        ###set newoutFileName="corrected."+str($outFileFormat)
+        ##--correctedFile $newoutFileName;
+        --correctedFile "corrected.bam";
+
+        mv $newoutFileName $outFileName
+    </command>
+    <inputs>
+        <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
+        <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>
+        <expand macro="reference_genome_source" />
+        <expand macro="effectiveGenomeSize" />
+
+        <!--
+        <param name="outFileFormat" type="select" label="File format of the output">
+            <option value="bam">bam</option>
+            <option value="bw">bigwig</option>
+            <option value="bg">bedgraph</option>
+        </param>
+        -->
+        <expand macro="region_limit_operation" />
+
+        <conditional name="advancedOpt">
+            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="binSize" type="integer" value="50" min="1" 
+                    label="Bin size in bp"
+                    help="Size of the bins in bp for the ouput of the bigwig/bedgraph file."/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="bam" name="outFileName">
+            <!--<change_format>
+                <when input="outFileFormat" value="bw" format="bigwig" />
+                <when input="outFileFormat" value="bam" format="bam" />
+                <when input="outFileFormat" value="bg" format="bedgraph" />
+            </change_format>-->
+        </data>
+    </outputs>
+    <help>
+
+**What it does**
+
+This tool requires the output from computeGCBias to correct the given BAM files according to the method proposed by Benjamini and Speed (2012). Nucleic Acids Res.
+The resulting BAM files can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.
+
+
+You can find more details in the `correctGCBias wiki`_.
+
+.. _correctGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias
+
+
+**Output files**:
+
+- GC-normalized BAM file
+
+-----
+
+@REFERENCES@
+
+    </help>
+</tool>