diff correctGCBias.xml @ 0:748076af9837 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/correctGCBias.xml	Mon Jan 25 20:23:49 2016 -0500
@@ -0,0 +1,75 @@
+<tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@WRAPPER_VERSION@.0">
+    <description>uses the output from computeGCBias to generate GC-corrected BAM files</description>
+    <macros>
+        <token name="@BINARY@">correctGCBias</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+        ln -s "$bamInput" "local_bamInput.bam" &&
+        ln -s "$bamInput.metadata.bam_index" local_bamInput.bam.bai &&
+
+        @BINARY@
+            @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 corrected.bam
+]]>
+    </command>
+    <inputs>
+        <param argument="--GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" help="" />
+        <param argument="--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" from_work_dir="corrected.bam" name="outFileName" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" />
+            <param name="bamInput" value="paired_chr2L.bam" ftype="bam" />
+            <param name="ref_source" value="history" />
+            <param name="input1" value="sequence.2bit" />
+            <param name="effectiveGenomeSize_opt" value="specific" />
+            <param name="effectiveGenomeSize" value="23011544" />
+            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" />
+        </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 in
+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 doc page: https://deeptools.readthedocs.org/en/master/content/tools/correctGCBias.html
+
+
+**Output files**:
+
+- GC-normalized BAM file
+
+-----
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>