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comparison mergeBed.xml @ 64:f6c88d2e9ae5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 071c1c5d4bad
children
comparison
equal deleted inserted replaced
63:7411007544bf 64:f6c88d2e9ae5
1 <tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <description>combine overlapping/nearby intervals into a single interval</description> 2 <description>combine overlapping/nearby intervals into a single interval</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools" /> 6 <expand macro="bio_tools" />
11 -i '${input}' 11 -i '${input}'
12 $strand 12 $strand
13 -d $distance 13 -d $distance
14 $header 14 $header
15 @C_AND_O_ARGUMENT@ 15 @C_AND_O_ARGUMENT@
16 #if $input.ext == "bam"
17 -bed
18 #end if
16 > '${output}' 19 > '${output}'
17 ]]></command> 20 ]]></command>
18 <inputs> 21 <inputs>
19 <param name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/> 22 <param name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Merge the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
20 <param name="strand" type="select" label="Calculation based on strandedness?"> 23 <param name="strand" type="select" label="Calculation based on strandedness?">
21 <option value="" selected="true">Overlaps on either strand</option> 24 <option value="" selected="true">Overlaps on either strand</option>
22 <option value="-s">Force strandedness. That is, only merge features that are the same strand (-s)</option> 25 <option value="-s">Force strandedness. That is, only merge features that are the same strand (-s)</option>
23 <option value="-S +">Force merge for forward strand only (-S +)</option> 26 <option value="-S +">Force merge for forward strand only (-S +)</option>
24 <option value="-S -">Force merge for reverse strand only (-S -)</option> 27 <option value="-S -">Force merge for reverse strand only (-S -)</option>
25 </param> 28 </param>
26 <param name="distance" argument="-d" type="integer" value="0" 29 <param name="distance" argument="-d" type="integer" value="0"
27 label="Maximum distance between features allowed for features to be merged" 30 label="Maximum distance between features allowed for features to be merged"
28 help="That is, overlapping and/or book-ended features are merged"/> 31 help="Default 0: overlapping and/or book-ended features are merged. Note: negative values enforce the number of b.p. required for overlap."/>
29 <expand macro="print_header" /> 32 <expand macro="print_header" />
30 <expand macro="c_and_o_argument"> 33 <expand macro="c_and_o_argument">
31 <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" /> 34 <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" />
32 </expand> 35 </expand>
33 </inputs> 36 </inputs>
36 </outputs> 39 </outputs>
37 <tests> 40 <tests>
38 <test> 41 <test>
39 <param name="input" value="mergedBed1.bed" ftype="bed" /> 42 <param name="input" value="mergedBed1.bed" ftype="bed" />
40 <output name="output" file="mergedBed_result1.bed" ftype="bed" /> 43 <output name="output" file="mergedBed_result1.bed" ftype="bed" />
44 <assert_command>
45 <not_has_text text="-s "/>
46 <not_has_text text="-S "/>
47 <has_text text="-d 0"/>
48 <not_has_text text="-c "/>
49 <not_has_text text="-o "/>
50 </assert_command>
41 </test> 51 </test>
42 <test> 52 <test>
43 <param name="input" value="mergedBed2.bed" ftype="bed" /> 53 <param name="input" value="mergedBed2.bed" ftype="bed" />
44 <param name="strand" value="-s" /> 54 <param name="strand" value="-s" />
45 <output name="output" file="mergedBed_result2.bed" ftype="bed" /> 55 <output name="output" file="mergedBed_result2.bed" ftype="bed" />
56 <assert_command>
57 <has_text text="-s "/>
58 <not_has_text text="-S "/>
59 <has_text text="-d 0"/>
60 <not_has_text text="-c "/>
61 <not_has_text text="-o "/>
62 </assert_command>
46 </test> 63 </test>
47 <test> 64 <test>
48 <param name="input" value="mergedBed3.bed" ftype="bed" /> 65 <param name="input" value="mergedBed3.bed" ftype="bed" />
49 <output name="output" file="mergedBed_result3.bed" ftype="bed" /> 66 <output name="output" file="mergedBed_result3.bed" ftype="bed" />
67 <assert_command>
68 <not_has_text text="-s "/>
69 <not_has_text text="-S "/>
70 <has_text text="-d 0"/>
71 <not_has_text text="-c "/>
72 <not_has_text text="-o "/>
73 </assert_command>
50 </test> 74 </test>
51 <test> 75 <test>
52 <param name="input" value="mergedBed4.bed" ftype="bed" /> 76 <param name="input" value="mergedBed4.bed" ftype="bed" />
53 <param name="distance" value="1000" /> 77 <param name="distance" value="1000" />
54 <output name="output" file="mergedBed_result4.bed" ftype="bed" /> 78 <output name="output" file="mergedBed_result4.bed" ftype="bed" />
79 <assert_command>
80 <not_has_text text="-s "/>
81 <not_has_text text="-S "/>
82 <has_text text="-d 1000"/>
83 <not_has_text text="-c "/>
84 <not_has_text text="-o "/>
85 </assert_command>
55 </test> 86 </test>
56 <test> 87 <test>
57 <param name="input" value="mergedBed4.bed" ftype="bed" /> 88 <param name="input" value="mergedBed4.bed" ftype="bed" />
58 <param name="distance" value="1000" /> 89 <param name="distance" value="1000" />
59 <repeat name="c_and_o_argument_repeat"> 90 <repeat name="c_and_o_argument_repeat">
60 <param name="col" value="1"/> 91 <param name="col" value="1"/>
61 <param name="operation" value="count"/> 92 <param name="operation" value="count"/>
62 </repeat> 93 </repeat>
63 <output name="output" file="mergedBed_result5.bed" ftype="bed" /> 94 <output name="output" file="mergedBed_result5.bed" ftype="bed" />
95 <assert_command>
96 <not_has_text text="-s "/>
97 <not_has_text text="-S "/>
98 <has_text text="-d 1000"/>
99 <has_text text="-c 1"/>
100 <has_text text="-o count"/>
101 </assert_command>
64 </test> 102 </test>
65 </tests> 103 </tests>
66 <help><![CDATA[ 104 <help><![CDATA[
67 **What it does** 105 **What it does**
68 106