Mercurial > repos > iuc > bedtools
comparison shuffleBed.xml @ 17:44867b59dbf2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
| author | iuc |
|---|---|
| date | Tue, 05 Sep 2017 15:40:14 -0400 |
| parents | 7308cc546a36 |
| children | a8eabd2838f6 |
comparison
equal
deleted
inserted
replaced
| 16:e0cec48a4695 | 17:44867b59dbf2 |
|---|---|
| 1 <tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0"> | 1 <tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.1"> |
| 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="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
| 8 <command> | 8 <command> |
| 9 <![CDATA[ | 9 <![CDATA[ |
| 10 bedtools shuffle | 10 bedtools shuffle |
| 11 -g '$genome' | 11 -g @GENOME_FILE@ |
| 12 -i '$inputA' | 12 -i '$inputA' |
| 13 $bedpe | 13 $bedpe |
| 14 #if str($seed.seed_choose) == "True": | 14 #if str($seed.seed_choose) == "True": |
| 15 -seed $seed.seed | 15 -seed $seed.seed |
| 16 #end if | 16 #end if |
| 29 ]]> | 29 ]]> |
| 30 </command> | 30 </command> |
| 31 <inputs> | 31 <inputs> |
| 32 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | 32 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> |
| 33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" /> | 33 <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" /> |
| 34 <expand macro="genome" /> | 34 <expand macro="input_conditional_genome_file" /> |
| 35 <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue="" | 35 <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue="" |
| 36 label="Keep features in the input file on the same chromosome" | 36 label="Keep features in the input file on the same chromosome" |
| 37 help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" /> | 37 help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" /> |
| 38 <expand macro="seed" /> | 38 <expand macro="seed" /> |
| 39 <conditional name="add_bed"> | 39 <conditional name="add_bed"> |
| 65 <data format="bed" name="output" /> | 65 <data format="bed" name="output" /> |
| 66 </outputs> | 66 </outputs> |
| 67 <tests> | 67 <tests> |
| 68 <test> | 68 <test> |
| 69 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> | 69 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> |
| 70 <param name="genome_file_opts_selector" value="hist" /> | |
| 70 <param name="genome" value="shuffleBed.len" ftype="tabular" /> | 71 <param name="genome" value="shuffleBed.len" ftype="tabular" /> |
| 71 <param name="chrom" value="" /> | 72 <param name="chrom" value="" /> |
| 72 <param name="seed_choose" value="True" /> | 73 <param name="seed_choose" value="True" /> |
| 73 <param name="seed" value="1" /> | 74 <param name="seed" value="1" /> |
| 74 <output name="output" file="shuffleBed_result1.bed" ftype="bed" /> | 75 <output name="output" file="shuffleBed_result1.bed" ftype="bed" /> |
| 75 </test> | 76 </test> |
| 76 <test> | 77 <test> |
| 77 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> | 78 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> |
| 79 <param name="genome_file_opts_selector" value="hist" /> | |
| 78 <param name="genome" value="shuffleBed.len" ftype="tabular" /> | 80 <param name="genome" value="shuffleBed.len" ftype="tabular" /> |
| 79 <param name="chrom" value="True" /> | 81 <param name="chrom" value="True" /> |
| 80 <param name="seed_choose" value="True" /> | 82 <param name="seed_choose" value="True" /> |
| 81 <param name="seed" value="1" /> | 83 <param name="seed" value="1" /> |
| 82 <output name="output" file="shuffleBed_result2.bed" ftype="bed" /> | 84 <output name="output" file="shuffleBed_result2.bed" ftype="bed" /> |
| 83 </test> | 85 </test> |
| 84 <test> | 86 <test> |
| 85 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> | 87 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> |
| 88 <param name="genome_file_opts_selector" value="hist" /> | |
| 86 <param name="genome" value="shuffleBed.len" ftype="tabular" /> | 89 <param name="genome" value="shuffleBed.len" ftype="tabular" /> |
| 87 <param name="excl" value="shuffleBed2.bed" ftype="bed" /> | 90 <param name="excl" value="shuffleBed2.bed" ftype="bed" /> |
| 88 <param name="seed_choose" value="True" /> | 91 <param name="seed_choose" value="True" /> |
| 89 <param name="seed" value="1" /> | 92 <param name="seed" value="1" /> |
| 90 <output name="output" file="shuffleBed_result3.bed" ftype="bed" /> | 93 <output name="output" file="shuffleBed_result3.bed" ftype="bed" /> |
| 91 </test> | 94 </test> |
| 92 <test> | 95 <test> |
| 93 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> | 96 <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> |
| 97 <param name="genome_file_opts_selector" value="hist" /> | |
| 94 <param name="genome" value="shuffleBed.len" ftype="bed" /> | 98 <param name="genome" value="shuffleBed.len" ftype="bed" /> |
| 95 <param name="allow_beyond" value="True" /> | 99 <param name="allow_beyond" value="True" /> |
| 96 <param name="seed_choose" value="True" /> | 100 <param name="seed_choose" value="True" /> |
| 97 <param name="seed" value="1" /> | 101 <param name="seed" value="1" /> |
| 98 <output name="output" file="shuffleBed_result4.bed" ftype="bed" /> | 102 <output name="output" file="shuffleBed_result4.bed" ftype="bed" /> |