Mercurial > repos > iuc > bedtools
annotate bedToBam.xml @ 16:e0cec48a4695 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ea1ac33f3337ac44f43150f585c9ccd38e08da0c
author | iuc |
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date | Fri, 18 Aug 2017 15:33:08 -0400 |
parents | 607c0576c6ab |
children | 44867b59dbf2 |
rev | line source |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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changeset
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1 <tool id="bedtools_bedtobam" name="BED to BAM" version="@WRAPPER_VERSION@.0"> |
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
diff
changeset
|
2 <description>converter</description> |
1 | 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" /> | |
4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
diff
changeset
|
34 <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" /> |
1 | 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> |