Mercurial > repos > bgruening > deeptools
annotate correctGCBias.xml @ 80:be73bb8a1303 draft default tip
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
| author | bgruening |
|---|---|
| date | Wed, 21 Oct 2015 02:51:49 -0400 |
| parents | 1dbd76a58d8b |
| children |
| rev | line source |
|---|---|
| 61 | 1 <tool id="deeptools_correctGCBias" name="correctGCBias" version="@WRAPPER_VERSION@.0"> |
| 2 <description>uses the output from computeGCBias to generate corrected BAM files</description> | |
| 3 <macros> | |
| 4 <token name="@BINARY@">correctGCBias</token> | |
| 5 <import>deepTools_macros.xml</import> | |
| 6 </macros> | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
7 <expand macro="requirements" /> |
| 61 | 8 <command> |
| 9 <![CDATA[ | |
| 10 ln -s $bamInput local_bamInput.bam; | |
| 11 ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai; | |
| 12 | |
| 13 correctGCBias | |
| 14 @THREADS@ | |
| 15 --bamfile local_bamInput.bam | |
| 16 --GCbiasFrequenciesFile $GCbiasFrequenciesFile | |
| 17 | |
| 18 @reference_genome_source@ | |
| 19 | |
| 20 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": | |
| 21 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize | |
| 22 #else: | |
| 23 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt | |
| 24 #end if | |
| 25 | |
| 26 #if str($region).strip() != '': | |
| 27 --region '$region' | |
| 28 #end if | |
|
66
1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
65
diff
changeset
|
29 --correctedFile corrected.bam; |
|
1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
65
diff
changeset
|
30 |
|
1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
65
diff
changeset
|
31 mv corrected.bam $outFileName; |
| 61 | 32 ]]> |
| 33 </command> | |
| 34 <inputs> | |
| 35 <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" /> | |
| 36 <param name="bamInput" format="bam" type="data" | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
37 label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted. (--bamfile)" /> |
| 61 | 38 <expand macro="reference_genome_source" /> |
| 39 <expand macro="effectiveGenomeSize" /> | |
| 40 <expand macro="region_limit_operation" /> | |
| 41 </inputs> | |
| 42 <outputs> | |
| 43 <data format="bam" name="outFileName" /> | |
| 44 </outputs> | |
| 45 <tests> | |
| 46 <test> | |
| 47 <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" /> | |
|
66
1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
65
diff
changeset
|
48 <param name="bamInput" value="paired_chr2L.bam" ftype="bam" /> |
| 61 | 49 <param name="ref_source" value="history" /> |
|
66
1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
65
diff
changeset
|
50 <param name="input1" value="sequence.2bit" /> |
| 61 | 51 <param name="effectiveGenomeSize_opt" value="specific" /> |
|
66
1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
65
diff
changeset
|
52 <param name="effectiveGenomeSize" value="23011544" /> |
|
1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
65
diff
changeset
|
53 <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" /> |
| 61 | 54 </test> |
| 55 </tests> | |
| 56 <help> | |
| 57 <![CDATA[ | |
| 58 **What it does** | |
| 59 | |
| 60 This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed by | |
| 61 Benjamini and Speed (2012) Nucleic Acids Res. | |
| 62 The resulting BAM file can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on. | |
| 63 | |
| 64 You can find more details on the correctGCBias wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias | |
| 65 | |
| 66 | |
| 67 **Output files**: | |
| 68 | |
| 69 - GC-normalized BAM file | |
| 70 | |
| 71 ----- | |
| 72 | |
| 73 @REFERENCES@ | |
| 74 ]]> | |
| 75 </help> | |
| 76 <expand macro="citations" /> | |
| 77 </tool> |