Mercurial > repos > iuc > bedtools
comparison annotateBed.xml @ 10:71af3ebbbb7a draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 29 Apr 2015 12:06:53 -0400 |
| parents | 0d3aa592ce27 |
| children | a2d4c30ba2f9 |
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| 9:21f1d1c5467b | 10:71af3ebbbb7a |
|---|---|
| 1 <tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0"> | |
| 2 <description></description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools annotate | |
| 11 -i "${inputA}" | |
| 12 #if $names.names_select == 'yes': | |
| 13 -files | |
| 14 #for $bed in $names.beds: | |
| 15 "${bed.input}" | |
| 16 #end for | |
| 17 | |
| 18 -names | |
| 19 #for $bed in $names.beds: | |
| 20 "${bed.inputName}" | |
| 21 #end for | |
| 22 #else: | |
| 23 #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] ) | |
| 24 -files "${files}" | |
| 25 #end if | |
| 26 $strand | |
| 27 $counts | |
| 28 $both | |
| 29 > "${output}" | |
| 30 ]]> | |
| 31 </command> | |
| 32 <inputs> | |
| 33 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" /> | |
| 34 <!-- Additional files, if the user needs more --> | |
| 35 <conditional name="names"> | |
| 36 <param name="names_select" type="select" label="Specify names for each file"> | |
| 37 <option value="no" selected="True">No</option> | |
| 38 <option value="yes">Yes</option> | |
| 39 </param> | |
| 40 <when value="yes"> | |
| 41 <repeat name="beds" title="Add BED files and names" > | |
| 42 <param name="input" format="bed" type="data" label="BED file" /> | |
| 43 <param name="inputName" type="text" label="Name of the file" /> | |
| 44 </repeat> | |
| 45 </when> | |
| 46 <when value="no"> | |
| 47 <param name="beds" format="bed" multiple="True" type="data" label="BED file" /> | |
| 48 </when> | |
| 49 </conditional> | |
| 50 <expand macro="strand2" /> | |
| 51 <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue="" | |
| 52 label="Report the count of features followed by the % coverage for each annotation file" | |
| 53 help="Default is to report solely the fraction of -i covered by each file." /> | |
| 54 <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue="" | |
| 55 label="Report the count of features followed by the % coverage for each annotation file" | |
| 56 help="Default is to report solely the fraction of the input file covered by each file." /> | |
| 57 </inputs> | |
| 58 <outputs> | |
| 59 <data format="bed" name="output" /> | |
| 60 </outputs> | |
| 61 <tests> | |
| 62 <test> | |
| 63 <param name="inputA" value="annotateBed1.bed" ftype="bed" /> | |
| 64 <param name="names_select" value="no" /> | |
| 65 <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed" /> | |
| 66 <output name="output" file="annotateBed_result.bed" ftype="bed" /> | |
| 67 </test> | |
| 68 </tests> | |
| 69 <help> | |
| 70 <![CDATA[ | |
| 71 **What it does** | |
| 72 | |
| 73 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. | |
| 74 | |
| 75 @REFERENCES@ | |
| 76 ]]> | |
| 77 </help> | |
| 78 <expand macro="citations" /> | |
| 79 </tool> |