diff correctGCBias.xml @ 61:f3140d17939e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/correctGCBias.xml	Fri Jan 23 16:53:31 2015 -0500
@@ -0,0 +1,76 @@
+<tool id="deeptools_correctGCBias" name="correctGCBias" version="@WRAPPER_VERSION@.0">
+    <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>
+<![CDATA[
+        ln -s $bamInput local_bamInput.bam;
+        ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;
+
+        correctGCBias
+            @THREADS@
+            --bamfile local_bamInput.bam
+            --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
+            --correctedFile $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" />
+        <expand macro="region_limit_operation" />
+    </inputs>
+    <outputs>
+        <data format="bam" name="outFileName" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" />
+            <param name="bamInput" value="phiX.bam" ftype="bam" />
+            <param name="ref_source" value="history" />
+            <param name="input1" value="phiX.2bit" />
+            <param name="effectiveGenomeSize_opt" value="specific" />
+            <param name="effectiveGenomeSize" value="5386" />
+            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed by
+Benjamini and Speed (2012) Nucleic Acids Res.
+The resulting BAM file 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 on the correctGCBias wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias
+
+
+**Output files**:
+
+- GC-normalized BAM file
+
+-----
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>