Mercurial > repos > iuc > bedtools
annotate makeWindowsBed.xml @ 35:ac2040a5e6ff draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
| author | iuc |
|---|---|
| date | Fri, 08 Dec 2017 03:26:23 -0500 |
| parents | b0d5e752c0c5 |
| children | d279800f4ff9 |
| rev | line source |
|---|---|
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35
ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents:
32
diff
changeset
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1 <tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.0"> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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4
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changeset
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2 <description>make interval windows across a genome</description> |
| 4 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools makewindows | |
| 11 #if $type.type_select == 'genome': | |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
26
diff
changeset
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12 @GENOME_FILE_MAKEWINDOWS@ |
| 4 | 13 #else: |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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17
diff
changeset
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14 -b '$type.input' |
| 4 | 15 #end if |
| 16 #if $action.action_select == 'windowsize': | |
| 17 -w $action.windowsize | |
| 18 #if $action.step_size.step_size_select == 'yes': | |
| 19 -s $action.step_size.step_size | |
| 20 #end if | |
| 21 #else: | |
| 22 -n $action.number | |
| 23 -s $action.step_size | |
| 24 #end if | |
| 25 $sourcename | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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26 > '$output' |
| 4 | 27 ]]> |
| 28 </command> | |
| 29 <inputs> | |
| 30 <conditional name="type"> | |
| 31 <param name="type_select" type="select" label="Work with"> | |
| 32 <option value="bed" selected="True">Bed File</option> | |
| 33 <option value="genome">Genome File</option> | |
| 34 </param> | |
| 35 <when value="bed"> | |
| 36 <param name="input" format="bed,vcf,gff,gff3" type="data" label="BED/VCF/GFF file"/> | |
| 37 </when> | |
| 38 <when value="genome"> | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
26
diff
changeset
|
39 <expand macro="input_conditional_genome_file" /> |
| 4 | 40 </when> |
| 41 </conditional> | |
| 42 <conditional name="action"> | |
| 43 <param name="action_select" type="select" label="Work with"> | |
| 44 <option value="windowsize" selected="True">Set WindowSize</option> | |
| 45 <option value="number">Give Number of Windows</option> | |
| 46 </param> | |
| 47 <when value="windowsize"> | |
| 48 <param name="windowsize" type="integer" value="1" | |
| 49 label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows" | |
| 50 help="i.e. same number of nucleotide in each window" /> | |
| 51 <conditional name="step_size"> | |
| 52 <param name="step_size_select" type="select" | |
| 53 label="Specify Step size? i.e. how many base pairs to step before creating a new window" | |
| 54 help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows)."> | |
| 55 <option value="yes">Yes</option> | |
| 56 <option value="no" selected="True">No</option> | |
| 57 </param> | |
| 58 <when value="yes"> | |
| 59 <param name="step_size" type="integer" value="100" label="Specify it" /> | |
| 60 </when> | |
| 61 <when value="no" /> | |
| 62 </conditional> | |
| 63 </when> | |
| 64 <when value="number"> | |
| 65 <param name="number" type="integer" value="1" | |
| 66 label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows" | |
| 67 help="i.e. same number of windows, with varying window sizes" /> | |
| 68 <param name="step_size" type="integer" value="100" label="Specify it" /> | |
| 69 </when> | |
| 70 </conditional> | |
| 71 <param name="sourcename" type="select" label="ID Naming Options"> | |
| 72 <option value="" selected="True">Default</option> | |
| 73 <option value="-i src">use the source interval's name</option> | |
| 74 <option value="-i winnum">use the window number as the ID (e.g. 1,2,3,4...)</option> | |
| 75 <option value="-i srcwinnum">use the source interval's name with the window number.</option> | |
| 76 </param> | |
| 77 </inputs> | |
| 78 <outputs> | |
| 79 <data name="output" format="bed" /> | |
| 80 </outputs> | |
| 81 <tests> | |
| 82 <test> | |
| 83 <param name="type_select" value="genome" /> | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
26
diff
changeset
|
84 <param name="genome_file_opts_selector" value="hist" /> |
| 4 | 85 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> |
| 86 <param name="action_select" value="windowsize" /> | |
| 87 <param name="windowsize" value="1000000" /> | |
| 88 <output name="output" file="makeWindowBed_result1.bed" ftype="bed" /> | |
| 89 </test> | |
| 90 <test> | |
| 91 <param name="type_select" value="genome" /> | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
26
diff
changeset
|
92 <param name="genome_file_opts_selector" value="hist" /> |
| 4 | 93 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> |
| 94 <param name="action_select" value="windowsize" /> | |
| 95 <param name="windowsize" value="1000000" /> | |
| 96 <param name="step_size_select" value="yes" /> | |
| 97 <param name="step_size" value="50000" /> | |
| 98 <output name="output" file="makeWindowBed_result2.bed" ftype="bed" /> | |
| 99 </test> | |
| 100 <test> | |
| 101 <param name="type_select" value="genome" /> | |
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32
b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
26
diff
changeset
|
102 <param name="genome_file_opts_selector" value="hist" /> |
| 4 | 103 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> |
| 104 <param name="action_select" value="number" /> | |
| 105 <param name="number" value="100" /> | |
| 106 <param name="step_size" value="10000" /> | |
| 107 <output name="output" file="makeWindowBed_result3.bed" ftype="bed" /> | |
| 108 </test> | |
| 109 <test> | |
| 110 <param name="type_select" value="bed" /> | |
| 111 <param name="input" value="makeWindowBed1.bed" ftype="bed" /> | |
| 112 <param name="action_select" value="number" /> | |
| 113 <param name="number" value="15" /> | |
| 114 <param name="step_size" value="100" /> | |
| 115 <output name="output" file="makeWindowBed_result4.bed" ftype="bed" /> | |
| 116 </test> | |
| 117 </tests> | |
| 118 <help> | |
| 119 <![CDATA[ | |
| 120 **What it does** | |
| 121 | |
| 122 Makes adjacent or sliding windows across a genome or BED file. | |
| 123 | |
| 124 @REFERENCES@ | |
| 125 ]]> | |
| 126 </help> | |
| 127 <expand macro="citations" /> | |
| 128 </tool> |