Mercurial > repos > brenninc > bedtools_bedtobam
comparison bedToBam.xml @ 0:a993f4a9aeaa draft default tip
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| author | brenninc |
|---|---|
| date | Thu, 12 May 2016 06:20:51 -0400 |
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| -1:000000000000 | 0:a993f4a9aeaa |
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| 1 <!-- adapted from https://toolshed.g2.bx.psu.edu/view/iuc/bedtools/f8b7dc21b4ee | |
| 2 Added the samtools sort and samtools requirement as bam files must be outpit sorted --> | |
| 3 <tool id="bedtools_bedtobam_sorted" name="BED to sorted BAM" version="@WRAPPER_VERSION@.0"> | |
| 4 <description>converter</description> | |
| 5 <macros> | |
| 6 <import>macros.xml</import> | |
| 7 </macros> | |
| 8 <expand macro="requirements" > | |
| 9 <requirement type="package" version="1.2">samtools</requirement> | |
| 10 </expand> | |
| 11 <expand macro="stdio" /> | |
| 12 <command> | |
| 13 <![CDATA[ | |
| 14 bedtools bedtobam | |
| 15 $bed12 | |
| 16 -mapq $mapq | |
| 17 -g $genome | |
| 18 -i '$input' | |
| 19 > unsorted.bam && | |
| 20 samtools sort -@ \${GALAXY_SLOTS:-1} -o '$output' -O bam -T dataset 'unsorted.bam' | |
| 21 ]]> | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/> | |
| 25 <param name="bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false" | |
| 26 label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format" | |
| 27 help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string. (-bed12)"/> | |
| 28 <expand macro="genome" /> | |
| 29 <param name="mapq" type="integer" value="255" | |
| 30 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" help="(-mapq)"/> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="input" value="bedToBam1.bed" ftype="bed" /> | |
| 38 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> | |
| 39 <output name="output" file="sortedBedToBam_result.bam" lines_diff="4" ftype="bam" /> | |
| 40 </test> | |
| 41 </tests> | |
| 42 <help> | |
| 43 <![CDATA[ | |
| 44 **What it does** | |
| 45 | |
| 46 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. | |
| 47 | |
| 48 @REFERENCES@ | |
| 49 ]]> | |
| 50 </help> | |
| 51 <expand macro="citations" /> | |
| 52 </tool> |