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comparison shuffleBed.xml @ 47:2892111d91f8 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 21:40:09 +0000
parents 64e2edfe7a2c
children
comparison
equal deleted inserted replaced
46:64e2edfe7a2c 47:2892111d91f8
1 <tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>randomly redistrubute intervals in a genome</description> 2 <description>randomly redistrubute intervals in a genome</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" />
9 <command><![CDATA[ 9 <command><![CDATA[
10 bedtools shuffle 10 bedtools shuffle
11 @GENOME_FILE@ 11 @GENOME_FILE@
12 -i '$inputA' 12 -i '$inputA'
13 $bedpe 13 $bedpe
14 #if str($seed.seed_choose) == "True": 14 #if str($seed) != "":
15 -seed $seed.seed 15 -seed $seed
16 #end if 16 #end if
17 #if str($add_bed.add_bed_select) == "not_be": 17 #if str($add_bed.add_bed_select) == "not_be":
18 -excl $add_bed.excl 18 -excl $add_bed.excl
19 #if str($add_bed.overlap) 19 #if str($add_bed.overlap)
20 -f $add_bed.overlap 20 -f $add_bed.overlap
66 <data name="output" format="bed" /> 66 <data name="output" format="bed" />
67 </outputs> 67 </outputs>
68 <tests> 68 <tests>
69 <test> 69 <test>
70 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> 70 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
71 <param name="genome_file_opts_selector" value="hist" /> 71 <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
72 <param name="genome" value="shuffleBed.len" ftype="tabular" /> 72 <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="tabular" />
73 <param name="chrom" value="" /> 73 <param name="chrom" value="false" />
74 <param name="seed_choose" value="True" />
75 <param name="seed" value="1" /> 74 <param name="seed" value="1" />
76 <output name="output" file="shuffleBed_result1.bed" ftype="bed" /> 75 <output name="output" file="shuffleBed_result1.bed" ftype="bed" />
77 </test> 76 </test>
78 <test> 77 <test>
79 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> 78 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
80 <param name="genome_file_opts_selector" value="hist" /> 79 <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
81 <param name="genome" value="shuffleBed.len" ftype="tabular" /> 80 <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="tabular" />
82 <param name="chrom" value="True" /> 81 <param name="chrom" value="True" />
83 <param name="seed_choose" value="True" />
84 <param name="seed" value="1" /> 82 <param name="seed" value="1" />
85 <output name="output" file="shuffleBed_result2.bed" ftype="bed" /> 83 <output name="output" file="shuffleBed_result2.bed" ftype="bed" />
86 </test> 84 </test>
87 <test> 85 <test>
88 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> 86 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
89 <param name="genome_file_opts_selector" value="hist" /> 87 <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
90 <param name="genome" value="shuffleBed.len" ftype="tabular" /> 88 <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="tabular" />
91 <conditional name="add_bed"> 89 <conditional name="add_bed">
92 <param name="add_bed_select" value="not_be"/> 90 <param name="add_bed_select" value="not_be"/>
93 <param name="excl" value="shuffleBed2.bed" ftype="bed" /> 91 <param name="excl" value="shuffleBed2.bed" ftype="bed" />
94 </conditional> 92 </conditional>
95 <param name="seed_choose" value="True" />
96 <param name="seed" value="1" /> 93 <param name="seed" value="1" />
97 <output name="output" file="shuffleBed_result3.bed" ftype="bed" /> 94 <output name="output" file="shuffleBed_result3.bed" ftype="bed" />
98 </test> 95 </test>
99 <test> 96 <test>
100 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> 97 <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
101 <param name="genome_file_opts_selector" value="hist" /> 98 <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
102 <param name="genome" value="shuffleBed.len" ftype="bed" /> 99 <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="bed" />
103 <param name="allow_beyond" value="True" /> 100 <param name="allow_beyond" value="True" />
104 <param name="seed_choose" value="True" />
105 <param name="seed" value="3" /> 101 <param name="seed" value="3" />
106 <output name="output" file="shuffleBed_result4.bed" ftype="bed" /> 102 <output name="output" file="shuffleBed_result4.bed" ftype="bed" />
107 </test> 103 </test>
108 </tests> 104 </tests>
109 <help><![CDATA[ 105 <help><![CDATA[