Mercurial > repos > bgruening > deeptools_compute_gc_bias
comparison computeGCBias.xml @ 8:1c9d626635b4 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
| author | bgruening |
|---|---|
| date | Tue, 20 Sep 2016 02:59:47 -0400 |
| parents | 12a3082cf023 |
| children | 4c03a58a512e |
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| 7:6a056fb2b9c1 | 8:1c9d626635b4 |
|---|---|
| 30 | 30 |
| 31 #if $advancedOpt.showAdvancedOpt == "yes": | 31 #if $advancedOpt.showAdvancedOpt == "yes": |
| 32 --sampleSize '$advancedOpt.sampleSize' | 32 --sampleSize '$advancedOpt.sampleSize' |
| 33 --regionSize '$advancedOpt.regionSize' | 33 --regionSize '$advancedOpt.regionSize' |
| 34 | 34 |
| 35 #if $advancedOpt.filterOut: | |
| 36 --filterOut $advancedOpt.filterOut | |
| 37 #end if | |
| 38 | |
| 39 #if $advancedOpt.extraSampling: | 35 #if $advancedOpt.extraSampling: |
| 40 --extraSampling $advancedOpt.extraSampling | 36 --extraSampling $advancedOpt.extraSampling |
| 41 #end if | 37 #end if |
| 38 | |
| 39 @blacklist@ | |
| 42 #end if | 40 #end if |
| 43 | 41 |
| 44 #if str($image_format) != 'none': | 42 #if str($image_format) != 'none': |
| 45 --biasPlot $outImageName | 43 --biasPlot $outImageName |
| 46 --plotFileFormat $image_format | 44 --plotFileFormat $image_format |
| 70 help ="To plot the reads per GC over a region, the size of the region is | 68 help ="To plot the reads per GC over a region, the size of the region is |
| 71 required (see below for more details about the method). By default, the bin size | 69 required (see below for more details about the method). By default, the bin size |
| 72 is set to 300 bases, which is close to the standard fragment size of many sequencing | 70 is set to 300 bases, which is close to the standard fragment size of many sequencing |
| 73 applications. However, if the depth of sequencing is low, a larger bin size will | 71 applications. However, if the depth of sequencing is low, a larger bin size will |
| 74 be required, otherwise many bins will not overlap with any read. (--regionSize)"/> | 72 be required, otherwise many bins will not overlap with any read. (--regionSize)"/> |
| 75 <param name="filterOut" type="data" format="bed" optional="true" | |
| 76 label="BED file containing genomic regions to be excluded from the estimation of the correction" | |
| 77 help="Such regions usually contain repetitive regions and peaks that, if included, would | |
| 78 bias the correction. It is recommended to filter out known repetitive regions if multi-reads | |
| 79 (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data, | |
| 80 it is recommended to first use a peak caller to identify and filter out the identified peaks. (--filterOut)" /> | |
| 81 <param name="extraSampling" type="data" format="bed" optional="true" | 73 <param name="extraSampling" type="data" format="bed" optional="true" |
| 82 label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome" | 74 label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome" |
| 83 help="(--extraSampling)" /> | 75 help="(--extraSampling)" /> |
| 76 <expand macro="blacklist" /> | |
| 84 </when> | 77 </when> |
| 85 </conditional> | 78 </conditional> |
| 86 <param name="image_format" type="select" | 79 <param name="image_format" type="select" |
| 87 label="GC bias plot" | 80 label="GC bias plot" |
| 88 help="If given, a diagnostic image summarizing the GC bias found on the sample will be created. (--plotFileFormat)"> | 81 help="If given, a diagnostic image summarizing the GC bias found on the sample will be created. (--plotFileFormat)"> |