Mercurial > repos > iuc > bedtools
comparison bedToBam.xml @ 1:82aac94b06c3 draft
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| author | iuc |
|---|---|
| date | Thu, 08 Jan 2015 14:25:51 -0500 |
| parents | |
| children | 607c0576c6ab |
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| 0:b8348686a0b9 | 1:82aac94b06c3 |
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| 1 <tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="@WRAPPER_VERSION@.0"> | |
| 2 <description></description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools bedtobam | |
| 11 $bed12 | |
| 12 -mapq $mapq | |
| 13 -g $genome | |
| 14 -i '$input' | |
| 15 > '$output' | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/> | |
| 20 <param name="bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false" | |
| 21 label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format" | |
| 22 help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string. (-bed12)"/> | |
| 23 <expand macro="genome" /> | |
| 24 <param name="mapq" type="integer" value="255" | |
| 25 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" help="(-mapq)"/> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="input" value="bedToBam1.bed" ftype="bed" /> | |
| 33 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> | |
| 34 <output name="output" file="bedToBam_result.bam" lines_diff="2" ftype="bam" /> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 <![CDATA[ | |
| 39 **What it does** | |
| 40 | |
| 41 bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes. | |
| 42 | |
| 43 @REFERENCES@ | |
| 44 ]]> | |
| 45 </help> | |
| 46 <expand macro="citations" /> | |
| 47 </tool> |