Mercurial > repos > iuc > bedtools
annotate fisherBed.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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1 <tool id="bedtools_fisher" name="FisherBed" 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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changeset
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2 <description>calculate Fisher statistic between two feature files</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 fisher | |
| 11 $strand | |
| 12 $split | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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17
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changeset
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13 -a '$inputA' |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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14 -b '$inputB' |
| 4 | 15 -f $overlap |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
26
diff
changeset
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16 -g @GENOME_FILE@ |
| 4 | 17 $reciprocal |
| 18 $m | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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19 > '$output' |
| 4 | 20 ]]> |
| 21 </command> | |
| 22 <inputs> | |
| 23 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | |
| 24 <param format="bed,gff,vcf,gff3" name="inputB" 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:
26
diff
changeset
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25 <expand macro="input_conditional_genome_file" /> |
| 4 | 26 <expand macro="strand2" /> |
| 27 <expand macro="split" /> | |
| 28 <expand macro="overlap" /> | |
| 29 <expand macro="reciprocal" /> | |
| 30 <param name="m" type="boolean" checked="False" truevalue="-m" falsevalue="" | |
| 31 label="Merge overlapping intervals before looking at overlap" help="(-m)" /> | |
| 32 </inputs> | |
| 33 <outputs> | |
| 34 <data name="output" metadata_source="inputA" format_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/> | |
| 35 </outputs> | |
| 36 <tests> | |
| 37 <test> | |
| 38 <param name="inputA" value="fisherBed1.bed" ftype="bed" /> | |
| 39 <param name="inputB" value="fisherBed2.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:
26
diff
changeset
|
40 <param name="genome_file_opts_selector" value="hist" /> |
| 4 | 41 <param name="genome" value="fisherBed.len" ftype="tabular" /> |
| 42 <output name="output" file="fisherBed_result1.bed" ftype="bed" /> | |
| 43 </test> | |
| 44 </tests> | |
| 45 <help> | |
| 46 <![CDATA[ | |
| 47 **What it does** | |
| 48 | |
| 49 Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files. | |
| 50 | |
| 51 @REFERENCES@ | |
| 52 ]]> | |
| 53 </help> | |
| 54 <expand macro="citations" /> | |
| 55 </tool> |