Mercurial > repos > bgruening > deeptools_bam_coverage
comparison bamCoverage.xml @ 1:66947f20a9a8 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
| author | bgruening |
|---|---|
| date | Fri, 18 Dec 2015 08:00:06 -0500 |
| parents | af2607db5c89 |
| children | 8c6f450d266c |
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| 0:af2607db5c89 | 1:66947f20a9a8 |
|---|---|
| 39 #if $advancedOpt.smoothLength: | 39 #if $advancedOpt.smoothLength: |
| 40 --smoothLength '$advancedOpt.smoothLength' | 40 --smoothLength '$advancedOpt.smoothLength' |
| 41 #end if | 41 #end if |
| 42 | 42 |
| 43 @ADVANCED_OPTS_READ_PROCESSING@ | 43 @ADVANCED_OPTS_READ_PROCESSING@ |
| 44 $advancedOpt.keepNAs | 44 $advancedOpt.skipNAs |
| 45 | 45 |
| 46 if str($advancedOpt.ignoreForNormalization).strip() != '': | 46 if str($advancedOpt.ignoreForNormalization).strip() != '': |
| 47 --ignoreForNormalization $advancedOpt.ignoreForNormalization | 47 --ignoreForNormalization $advancedOpt.ignoreForNormalization |
| 48 end if | 48 end if |
| 49 #end if | 49 #end if |
| 96 containing those chromosomes that should be excluded | 96 containing those chromosomes that should be excluded |
| 97 for computing the normalization. This is useful when | 97 for computing the normalization. This is useful when |
| 98 considering samples with unequal coverage across | 98 considering samples with unequal coverage across |
| 99 chromosomes like male samples. Example: chrX chrM" /> | 99 chromosomes like male samples. Example: chrX chrM" /> |
| 100 | 100 |
| 101 <expand macro="keepNAs" /> | 101 <expand macro="skipNAs" /> |
| 102 <expand macro="read_processing_options" /> | 102 <expand macro="read_processing_options" /> |
| 103 | 103 |
| 104 <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue="" | 104 <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue="" |
| 105 label="Determine nucleosome positions from MNase-seq data" | 105 label="Determine nucleosome positions from MNase-seq data" |
| 106 help="Only 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." /> | 106 help="Only 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." /> |