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comparison annotateBed.xml @ 4:315929597efb draft

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author iuc
date Wed, 07 Jan 2015 12:45:05 -0500
parents 7511823bdea1
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3:190a747ddaa8 4:315929597efb
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[
9 bedtools annotate 10 bedtools annotate
10 -i $inputA 11 -i "${inputA}"
11 -files 12 #if $names.names_select == 'yes':
12 #for $bed in $names.beds: 13 -files
13 $bed.input 14 #for $bed in $names.beds:
14 #end for 15 "${bed.input}"
16 #end for
15 17
16 #if $names.names_select == 'yes':
17 -names 18 -names
18 #for $bed in $names.beds: 19 #for $bed in $names.beds:
19 $bed.inputName 20 "${bed.inputName}"
20 #end for 21 #end for
22 #else:
23 #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
24 -files "${files}"
21 #end if 25 #end if
22 $strand 26 $strand
23 $counts 27 $counts
24 $both 28 $both
25 &gt; $output 29 > "${output}"
30 ]]>
26 </command> 31 </command>
27 <inputs> 32 <inputs>
28 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" /> 33 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" />
29 <!-- Additional files, if the user needs more --> 34 <!-- Additional files, if the user needs more -->
30 <conditional name="names"> 35 <conditional name="names">
37 <param name="input" format="bed" type="data" label="BED file" /> 42 <param name="input" format="bed" type="data" label="BED file" />
38 <param name="inputName" type="text" label="Name of the file" /> 43 <param name="inputName" type="text" label="Name of the file" />
39 </repeat> 44 </repeat>
40 </when> 45 </when>
41 <when value="no"> 46 <when value="no">
42 <repeat name="beds" title="Add BED files" > 47 <param name="beds" format="bed" multiple="True" type="data" label="BED file" />
43 <param name="input" format="bed" type="data" label="BED file" />
44 </repeat>
45 </when> 48 </when>
46 </conditional> 49 </conditional>
47
48 <expand macro="strand2" /> 50 <expand macro="strand2" />
49 <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue="" label="Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of -i covered by each file." /> 51 <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue=""
50 <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue="" label="Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of the input file covered by each file." /> 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." />
51 </inputs> 57 </inputs>
52
53 <outputs> 58 <outputs>
54 <data format="bed" name="output" label="" /> 59 <data format="bed" name="output" />
55 </outputs> 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>
56 <help> 69 <help>
57 70 <![CDATA[
58 **What it does** 71 **What it does**
59 72
60 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. 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.
61 74
62 @REFERENCES@ 75 @REFERENCES@
63 76 ]]>
64 </help> 77 </help>
65 <expand macro="citations" /> 78 <expand macro="citations" />
66 </tool> 79 </tool>