Mercurial > repos > iuc > bedtools
annotate bedpeToBam.xml @ 17:a2d4c30ba2f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
| author | iuc |
|---|---|
| date | Sun, 21 Jun 2015 22:49:46 -0400 |
| parents | 0d3aa592ce27 |
| children | b0d5e752c0c5 |
| rev | line source |
|---|---|
|
17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
|
1 <tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.0"> |
|
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
|
2 <description>converter</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools bedpetobam | |
| 11 -mapq $mapq | |
| 12 -i '$input' | |
| 13 -g $genome | |
| 14 > '$output' | |
| 15 ]]> | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/> | |
| 19 <expand macro="genome" /> | |
| 20 <param name="mapq" type="integer" value="255" | |
| 21 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" | |
| 22 help="(-mapq)" /> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data format="bam" name="output" metadata_source="input"/> | |
| 26 </outputs> | |
| 27 <tests> | |
| 28 <test> | |
| 29 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" /> | |
| 30 <param name="genome" value="mm9.len"/> | |
| 31 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" /> | |
| 32 </test> | |
| 33 </tests> | |
| 34 <help> | |
| 35 <![CDATA[ | |
| 36 **What it does** | |
| 37 | |
| 38 Converts feature records to BAM format. | |
| 39 | |
| 40 .. class:: warningmark | |
| 41 | |
| 42 BED files must be at least BED4 to create BAM (needs name field). | |
| 43 | |
| 44 @REFERENCES@ | |
| 45 ]]> | |
| 46 </help> | |
| 47 <expand macro="citations" /> | |
| 48 </tool> |