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comparison coverageBed.xml @ 18:18aeac3cd1db draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit dc0d10f28180ec2b2d1b0beac637601ea859e8f2
author iuc
date Sat, 21 Oct 2017 07:57:53 -0400
parents 7308cc546a36
children a8eabd2838f6
comparison
equal deleted inserted replaced
17:44867b59dbf2 18:18aeac3cd1db
1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
2 <description>of features in file B on the features in file A (bedtools coverage)</description> 2 <description>of features in file B on the features in file A (bedtools coverage)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
12 bedtools coverage 12 bedtools coverage
13 $d 13 $d
14 $hist 14 $hist
15 $split 15 $split
16 $strandedness 16 $strandedness
17 #if str($overlap_a) != "None" and str($overlap_a):
18 -f '$overlap_a'
19 #end if
20 #if str($overlap_b) != "None" and str($overlap_b):
21 -F '$overlap_b'
22 #end if
23 $reciprocal_overlap
24 $a_or_b
17 -a '$inputA' 25 -a '$inputA'
18 -b '$inputBs' 26 -b '$inputBs'
19 | sort -k1,1 -k2,2n 27 | sort -k1,1 -k2,2n
20 > '$output' 28 > '$output'
21 ]]> 29 ]]>
30 label="Report the depth at each position in each A feature" 38 label="Report the depth at each position in each A feature"
31 help="Positions reported are one based. Each position and depth follow the complete B feature (-d)" /> 39 help="Positions reported are one based. Each position and depth follow the complete B feature (-d)" />
32 <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue="" 40 <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue=""
33 label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A" 41 label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
34 help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth (-hist)" /> 42 help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth (-hist)" />
43 <param name="overlap_a" type="text"
44 label="Minimum overlap required as a fraction of A."
45 help="Default is 1E-9 (i.e., 1bp). (-f)">
46 <sanitizer invalid_char="">
47 <valid initial="string.digits"><add value=",."/></valid>
48 </sanitizer>
49 </param>
50 <param name="overlap_b" type="text"
51 label="Minimum overlap required as a fraction of B."
52 help="Default is 1E-9 (i.e., 1bp). (-F)">
53 <sanitizer invalid_char="">
54 <valid initial="string.digits"><add value=",."/></valid>
55 </sanitizer>
56 </param>
57 <param name="reciprocal_overlap" type="boolean" checked="false" truevalue="-r" falsevalue=""
58 label="Require that the fraction overlap be reciprocal for A AND B."
59 help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B (-r)" />
60 <param name="a_or_b" type="boolean" checked="false" truevalue="-e" falsevalue=""
61 label="Require that the minimum fraction be satisfied for A OR B."
62 help="if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied. (-e)" />
35 </inputs> 63 </inputs>
36 <outputs> 64 <outputs>
37 <data format="bed" name="output" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/> 65 <data format="bed" name="output" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
38 </outputs> 66 </outputs>
39 <tests> 67 <tests>
40 <test> 68 <test>
41 <param name="inputA" value="coverageBedA.bed" ftype="bed" /> 69 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
42 <param name="genome" value="coverageBedB.bed" ftype="bed" /> 70 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
43 <output name="output" file="coverageBed_result1.bed" ftype="bed" /> 71 <output name="output" file="coverageBed_result1.bed" ftype="bed" />
72 </test>
73 <test>
74 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
75 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
76 <param name="overlap_b" value="1" />
77 <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" />
78 </test>
79 <test>
80 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
81 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
82 <param name="overlap_a" value="1" />
83 <param name="reciprocal_overlap" value="true" />
84 <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />
44 </test> 85 </test>
45 </tests> 86 </tests>
46 <help> 87 <help>
47 <![CDATA[ 88 <![CDATA[
48 **What it does** 89 **What it does**