Mercurial > repos > bgruening > deeptools_bam_pe_fragmentsize
comparison bamPEFragmentSize.xml @ 0:bb2b0ad44c0e draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
| author | bgruening |
|---|---|
| date | Mon, 25 Jan 2016 20:14:03 -0500 |
| parents | |
| children | 011ea45dda07 |
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| -1:000000000000 | 0:bb2b0ad44c0e |
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| 1 <tool id="deeptools_bam_pe_fragmentsize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0"> | |
| 2 <description>Estimate the paired-end fragment length in a BAM file</description> | |
| 3 <macros> | |
| 4 <token name="@BINARY@">bamPEFragmentSize</token> | |
| 5 <import>deepTools_macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 ln -s $bamInput one.bam && | |
| 11 ln -s '${bamInput.metadata.bam_index}' one.bam.bai && | |
| 12 | |
| 13 @BINARY@ | |
| 14 @THREADS@ | |
| 15 #if $histogram: | |
| 16 --histogram ./hist.png | |
| 17 #end if | |
| 18 --plotTitle "$plotTitle" | |
| 19 one.bam | |
| 20 > $outfile | |
| 21 ]]> | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param name="bamInput" format="bam" type="data" label="BAM file" | |
| 25 help="The BAM file must be sorted."/> | |
| 26 <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue="" | |
| 27 label="Get the distribution of fragment lengths as a histogram" | |
| 28 help=""/> | |
| 29 <expand macro="plotTitle" /> | |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 <data name="outfile" format="txt"/> | |
| 33 <data name="histogram_outfile" from_work_dir="hist.png" format="png"> | |
| 34 <filter>histogram is True</filter> | |
| 35 </data> | |
| 36 </outputs> | |
| 37 <tests> | |
| 38 <test> | |
| 39 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" /> | |
| 40 <param name="histogram" value="True" /> | |
| 41 <param name="plotTitle" value="Test Plot" /> | |
| 42 <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" /> | |
| 43 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" /> | |
| 44 </test> | |
| 45 </tests> | |
| 46 <help> | |
| 47 <![CDATA[ | |
| 48 **What it does** | |
| 49 | |
| 50 This tool samples a BAM file containing paired-end data to estimate the fragment length distribution. | |
| 51 Properly paired reads are preferred for computation. The output can be obtained as a histogram. | |
| 52 | |
| 53 ----- | |
| 54 | |
| 55 @REFERENCES@ | |
| 56 ]]> | |
| 57 </help> | |
| 58 <expand macro="citations" /> | |
| 59 </tool> |