Mercurial > repos > iuc > bedtools
annotate bedToBam.xml @ 48:2f457890d8c8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
| author | iuc |
|---|---|
| date | Tue, 11 Dec 2018 13:59:34 -0500 |
| parents | ac2040a5e6ff |
| children | df28283b3778 |
| rev | line source |
|---|---|
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48
2f457890d8c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
35
diff
changeset
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1 <tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@WRAPPER_VERSION@"> |
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17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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4
diff
changeset
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2 <description>converter</description> |
| 4 | 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 $mapq | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
17
diff
changeset
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13 -g @GENOME_FILE@ |
| 4 | 14 -i '$input' |
| 15 > '$output' | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/> | |
| 20 <param name="bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false" | |
| 21 label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format" | |
| 22 help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string. (-bed12)"/> | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
17
diff
changeset
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23 <expand macro="input_conditional_genome_file" /> |
| 4 | 24 <param name="mapq" type="integer" value="255" |
| 25 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" help="(-mapq)"/> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="input" value="bedToBam1.bed" ftype="bed" /> | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
17
diff
changeset
|
33 <param name="genome_file_opts_selector" value="hist" /> |
| 4 | 34 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> |
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17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
4
diff
changeset
|
35 <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" /> |
| 4 | 36 </test> |
| 37 </tests> | |
| 38 <help> | |
| 39 <![CDATA[ | |
| 40 **What it does** | |
| 41 | |
| 42 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. | |
| 43 | |
| 44 @REFERENCES@ | |
| 45 ]]> | |
| 46 </help> | |
| 47 <expand macro="citations" /> | |
| 48 </tool> |