Mercurial > repos > bgruening > deeptools_correct_gc_bias
diff correctGCBias.xml @ 0:748076af9837 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author | bgruening |
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date | Mon, 25 Jan 2016 20:23:49 -0500 |
parents | |
children | 4930eb430843 |
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--- /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>