Mercurial > repos > iuc > bedtools
annotate annotateBed.xml @ 11:7308cc546a36 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
| author | iuc |
|---|---|
| date | Mon, 17 Oct 2016 10:13:35 -0400 |
| parents | 607c0576c6ab |
| children | 95a3b2c25bd1 |
| rev | line source |
|---|---|
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
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1 <tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0"> |
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4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
diff
changeset
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2 <description>annotate coverage of features from multiple files</description> |
| 0 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 1 | 9 <![CDATA[ |
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4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
diff
changeset
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10 |
| 0 | 11 bedtools annotate |
| 1 | 12 -i "${inputA}" |
| 13 #if $names.names_select == 'yes': | |
| 14 -files | |
| 15 #for $bed in $names.beds: | |
| 16 "${bed.input}" | |
| 17 #end for | |
| 0 | 18 |
| 19 -names | |
| 20 #for $bed in $names.beds: | |
| 1 | 21 "${bed.inputName}" |
| 0 | 22 #end for |
| 1 | 23 #else: |
| 24 #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] ) | |
| 25 -files "${files}" | |
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4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
diff
changeset
|
26 #set names = '" "'.join( [ str( $name.display_name ) for $name in $names.beds ] ) |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
diff
changeset
|
27 -names "${names}" |
| 0 | 28 #end if |
| 29 $strand | |
| 30 $counts | |
| 31 $both | |
| 1 | 32 > "${output}" |
| 33 ]]> | |
| 0 | 34 </command> |
| 35 <inputs> | |
| 36 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" /> | |
| 37 <!-- Additional files, if the user needs more --> | |
| 38 <conditional name="names"> | |
| 39 <param name="names_select" type="select" label="Specify names for each file"> | |
| 40 <option value="no" selected="True">No</option> | |
| 41 <option value="yes">Yes</option> | |
| 42 </param> | |
| 43 <when value="yes"> | |
| 44 <repeat name="beds" title="Add BED files and names" > | |
| 45 <param name="input" format="bed" type="data" label="BED file" /> | |
| 46 <param name="inputName" type="text" label="Name of the file" /> | |
| 47 </repeat> | |
| 48 </when> | |
| 49 <when value="no"> | |
| 1 | 50 <param name="beds" format="bed" multiple="True" type="data" label="BED file" /> |
| 0 | 51 </when> |
| 52 </conditional> | |
| 53 <expand macro="strand2" /> | |
| 1 | 54 <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue="" |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
55 label="Report the count of features followed by the % coverage for each annotation file" |
| 1 | 56 help="Default is to report solely the fraction of -i covered by each file." /> |
| 57 <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue="" | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
58 label="Report the count of features followed by the % coverage for each annotation file" |
| 1 | 59 help="Default is to report solely the fraction of the input file covered by each file." /> |
| 0 | 60 </inputs> |
| 61 <outputs> | |
| 1 | 62 <data format="bed" name="output" /> |
| 0 | 63 </outputs> |
| 1 | 64 <tests> |
| 65 <test> | |
| 66 <param name="inputA" value="annotateBed1.bed" ftype="bed" /> | |
| 67 <param name="names_select" value="no" /> | |
| 68 <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed" /> | |
| 69 <output name="output" file="annotateBed_result.bed" ftype="bed" /> | |
| 70 </test> | |
| 71 </tests> | |
| 0 | 72 <help> |
| 1 | 73 <![CDATA[ |
| 0 | 74 **What it does** |
| 75 | |
| 76 bedtools annotate, well, annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command. | |
| 77 | |
| 78 @REFERENCES@ | |
| 1 | 79 ]]> |
| 0 | 80 </help> |
| 81 <expand macro="citations" /> | |
| 82 </tool> |