Mercurial > repos > iuc > bedtools
annotate complementBed.xml @ 41:c96688f1746d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ee522a02a3fab980a5b32a1387182c951ab04968
| author | iuc |
|---|---|
| date | Fri, 20 Apr 2018 05:30:04 -0400 |
| parents | ac2040a5e6ff |
| children | d279800f4ff9 |
| rev | line source |
|---|---|
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
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32
diff
changeset
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1 <tool id="bedtools_complementbed" name="ComplementBed" version="@WRAPPER_VERSION@.0"> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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8
diff
changeset
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2 <description>Extract intervals not represented by an interval file</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 complementBed | |
| 11 -i "$input" | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
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17
diff
changeset
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12 -g @GENOME_FILE@ |
| 8 | 13 > "$output" |
| 14 ]]> | |
| 15 </command> | |
| 16 <inputs> | |
| 17 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> | |
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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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18 <expand macro="input_conditional_genome_file" /> |
| 8 | 19 </inputs> |
| 20 <outputs> | |
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41
c96688f1746d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ee522a02a3fab980a5b32a1387182c951ab04968
iuc
parents:
35
diff
changeset
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21 <data format_source="input" name="output" metadata_source="input" label="Complement of ${input.name}"/> |
| 8 | 22 </outputs> |
| 23 <tests> | |
| 24 <test> | |
| 25 <param name="input" value="a.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
|
26 <param name="genome_file_opts_selector" value="hist" /> |
| 8 | 27 <param name="genome" value="mm9_chr1.len" /> |
| 28 <output name="output" file="complementBed_result1.bed" ftype="bed" /> | |
| 29 </test> | |
| 30 </tests> | |
| 31 <help> | |
| 32 <![CDATA[ | |
| 33 **What it does** | |
| 34 | |
| 35 bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. | |
| 36 | |
| 37 .. image:: $PATH_TO_IMAGES/complement-glyph.png | |
| 38 | |
| 39 @REFERENCES@ | |
| 40 ]]> | |
| 41 </help> | |
| 42 <expand macro="citations" /> | |
| 43 </tool> |