Mercurial > repos > bgruening > deeptools
annotate bamPEFragmentSize.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_bamPEFragmentSize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0"> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
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2 <description>Given a BAM file it samples several regions to estimate the paired-end fragment length</description> |
| 61 | 3 <macros> |
| 4 <token name="@BINARY@">bamPEFragmentSize</token> | |
| 5 <import>deepTools_macros.xml</import> | |
| 6 </macros> | |
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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 bamPEFragmentSize | |
| 11 @THREADS@ | |
| 12 -bai ${bamInput.metadata.bam_index} | |
| 13 #if $histogram: | |
| 14 --histogram ./hist.png | |
| 15 #end if | |
| 16 '$bamInput' | |
| 17 > $outfile | |
| 18 ]]> | |
| 19 </command> | |
| 20 <inputs> | |
| 21 <param name="bamInput" format="bam" type="data" label="BAM file" | |
| 22 help="The BAM file must be sorted."/> | |
| 23 <param name="histogram" type="boolean" truevalue="--histogram" falsevalue="" | |
| 24 label="Get the distribion of fragment length as histogram" | |
| 25 help="(--histogram)"/> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data name="outfile" format="txt"/> | |
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65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
29 <data name="histogram_outfile" from_work_dir="hist.png" format="png"> |
| 61 | 30 <filter>histogram is True</filter> |
| 31 </data> | |
| 32 </outputs> | |
| 33 <tests> | |
| 34 <test> | |
| 35 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" /> | |
| 36 <param name="histogram" value="True" /> | |
| 37 <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" /> | |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
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diff
changeset
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38 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" /> |
| 61 | 39 </test> |
| 40 </tests> | |
| 41 <help> | |
| 42 <![CDATA[ | |
| 43 **What it does** | |
| 44 | |
| 45 Given a BAM file it samples several regions to estimate the paird-end fragment length. | |
| 46 | |
| 47 ----- | |
| 48 | |
| 49 @REFERENCES@ | |
| 50 ]]> | |
| 51 </help> | |
| 52 <expand macro="citations" /> | |
| 53 </tool> |