Mercurial > repos > bgruening > deeptools_bam_pe_fragmentsize
comparison bamPEFragmentSize.xml @ 3:6da6f2908463 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
| author | bgruening |
|---|---|
| date | Wed, 09 Mar 2016 17:49:50 -0500 |
| parents | 011ea45dda07 |
| children | a14f74993305 |
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| 2:ef131d53cbdf | 3:6da6f2908463 |
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| 24 > $outfile | 24 > $outfile |
| 25 ]]> | 25 ]]> |
| 26 </command> | 26 </command> |
| 27 <inputs> | 27 <inputs> |
| 28 <param name="bamInput" format="bam" type="data" label="BAM file" | 28 <param name="bamInput" format="bam" type="data" label="BAM file" |
| 29 help="The BAM file must be sorted."/> | 29 help=""/> |
| 30 <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue="" | 30 <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue="" |
| 31 label="Get the distribution of fragment lengths as a histogram" | 31 label="Get the distribution of fragment lengths as a histogram" |
| 32 help=""/> | 32 help=""/> |
| 33 <expand macro="plotTitle" /> | 33 <expand macro="plotTitle" /> |
| 34 <conditional name="advancedOpt"> | 34 <conditional name="advancedOpt"> |
| 64 </tests> | 64 </tests> |
| 65 <help> | 65 <help> |
| 66 <![CDATA[ | 66 <![CDATA[ |
| 67 | 67 |
| 68 What it does | 68 What it does |
| 69 --------------- | 69 ------------ |
| 70 | 70 |
| 71 This tool samples a BAM file with paired-end data to estimate the fragment length distribution. | 71 This tool samples a BAM file with paired-end data to estimate the fragment length distribution. |
| 72 Properly paired reads are preferred for computation, i.e., unless a region does not contain any concordant pairs, discordant pairs are ignored. | 72 Properly paired reads are preferred for computation, i.e., unless a region does not contain any concordant pairs, discordant pairs are ignored. |
| 73 | 73 |
| 74 Output | 74 Output |
| 75 ---------- | 75 ------ |
| 76 | 76 |
| 77 The **default** output is a simple summary statistic for the observed fragment lengths. | 77 The **default** output is a simple summary statistic for the observed fragment lengths. |
| 78 | 78 |
| 79 Optionally, you can obtain a histogram of fragment sizes, which will give you a better idea of the distribution of fragment lengths. | 79 Optionally, you can obtain a histogram of fragment sizes, which will give you a better idea of the distribution of fragment lengths. |
| 80 | 80 |