Mercurial > repos > iuc > bedtools
annotate multiIntersectBed.xml @ 42:d279800f4ff9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
| author | iuc |
|---|---|
| date | Thu, 26 Apr 2018 17:02:24 -0400 |
| parents | ac2040a5e6ff |
| children | 2f457890d8c8 |
| rev | line source |
|---|---|
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
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changeset
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1 <tool id="bedtools_multiintersectbed" name="Multiple Intersect" 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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2 <description>identifies common intervals among multiple interval files</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools multiinter | |
| 11 $header | |
| 12 $cluster | |
| 13 -filler "${filler}" | |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
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14 $empty.empty_selector |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
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15 @GENOME_FILE_UNION@ |
| 8 | 16 |
| 17 #if str($tag.tag_select) == "tag": | |
| 18 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] ) | |
| 19 -i "${files}" | |
| 20 #else: | |
| 21 -i | |
| 22 #for $file in $tag.beds: | |
| 23 "${file.input}" | |
| 24 #end for | |
| 25 -names | |
| 26 #for $file in $tag.beds: | |
| 27 "{$file.custom_name}" | |
| 28 #end for | |
| 29 #end if | |
| 30 | |
| 31 > '$output' | |
| 32 ]]> | |
| 33 </command> | |
| 34 <inputs> | |
| 35 <conditional name="tag"> | |
| 36 <param name="tag_select" type="select" label="Sample name"> | |
| 37 <option value="tag" selected="true">Use input's tag</option> | |
| 38 <option value="custom">Enter custom name per file</option> | |
| 39 </param> | |
| 40 <when value="tag"> | |
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d279800f4ff9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
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41 <param name="inputs" format="@STD_BEDTOOLS_INPUTS@" type="data" multiple="True" label="@STD_BEDTOOLS_INPUT_LABEL@ files" /> |
| 8 | 42 </when> |
| 43 <when value="custom"> | |
| 44 <repeat name="beds" title="Add BED files" min="2" > | |
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d279800f4ff9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
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45 <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" multiple="True" label="@STD_BEDTOOLS_INPUT_LABEL@ file" /> |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
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46 <param name="custom_name" type="text" area="false" label="Custom sample name" /> |
| 8 | 47 </repeat> |
| 48 </when> | |
| 49 </conditional> | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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50 <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue="" |
| 8 | 51 label="Invoke Ryan Layers's clustering algorithm" |
| 52 help="(-cluster)" /> | |
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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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53 <conditional name="empty"> |
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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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54 <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets"> |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
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changeset
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55 <option value="-empty">Yes</option> |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
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changeset
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56 <option value="">No</option> |
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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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57 </param> |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
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changeset
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58 <when value="-empty"> |
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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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59 <expand macro="input_conditional_genome_file" /> |
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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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60 </when> |
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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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61 <when value="" /> |
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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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62 </conditional> |
| 8 | 63 <param name="filler" type="text" value="N/A" |
| 64 label="Text to use for no-coverage value" | |
| 65 help="Can be 0.0, N/A, - or any other value. (-filler)" /> | |
| 66 <expand macro="print_header" /> | |
| 67 | |
| 68 </inputs> | |
| 69 <outputs> | |
| 70 <data format="bed" name="output" /> | |
| 71 </outputs> | |
| 72 <tests> | |
| 73 <test> | |
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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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74 <param name="tag_select" value="tag" /> |
| 8 | 75 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> |
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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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76 <param name="empty_selector" value="" /> |
| 8 | 77 <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" /> |
| 78 </test> | |
| 79 <test> | |
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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
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80 <param name="tag_select" value="tag" /> |
| 8 | 81 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> |
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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
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82 <param name="header" value="True" /> |
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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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83 <param name="empty_selector" value="" /> |
| 8 | 84 <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" /> |
| 85 </test> | |
| 86 <test> | |
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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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87 <param name="tag_select" value="tag" /> |
| 8 | 88 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> |
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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
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89 <param name="empty_selector" value="-empty" /> |
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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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90 <param name="genome_file_opts_selector" value="hist" /> |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
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diff
changeset
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91 <param name="genome" value="multiIntersectBed1.len" /> |
| 8 | 92 <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" /> |
| 93 </test> | |
| 94 </tests> | |
| 95 <help> | |
| 96 <![CDATA[ | |
| 97 **What it does** | |
| 98 | |
| 99 This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files. | |
| 100 | |
| 101 | |
| 102 .. class:: warningmark | |
| 103 | |
| 104 This tool requires that each BED file is reference-sorted (chrom, then start). | |
| 105 | |
| 106 | |
| 107 .. class:: infomark | |
| 108 | |
| 109 The output file will contain five fixed columns, plus additional columns for each BED file: | |
| 110 | |
| 111 * 1. Chromosome name (or 'genome' for whole-genome coverage). | |
| 112 * 2. The zero-based start position of the interval. | |
| 113 * 3. The one-based end position of the interval. | |
| 114 * 4. The number of input files that had at least one feature overlapping this interval. | |
| 115 * 5. A list of input files or labels that had at least one feature overlapping this interval. | |
| 116 * 6. For each input file, an indication (1 = Yes, 0 = No) of whether or not the file had at least one feature overlapping this interval. | |
| 117 | |
| 118 ------ | |
| 119 | |
| 120 **Example input**:: | |
| 121 | |
| 122 # a.bed | |
| 123 chr1 6 12bed | |
| 124 chr1 10 20 | |
| 125 chr1 22 27 | |
| 126 chr1 24 30 | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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changeset
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127 |
| 8 | 128 # b.bed |
| 129 chr1 12 32 | |
| 130 chr1 14 30 | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
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diff
changeset
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131 |
| 8 | 132 # c.bed |
| 133 chr1 8 15 | |
| 134 chr1 10 14 | |
| 135 chr1 32 34 | |
| 136 | |
| 137 | |
| 138 ------ | |
| 139 | |
| 140 **Example without a header and without reporting intervals with zero coverage**:: | |
| 141 | |
| 142 | |
| 143 chr1 6 8 1 1 1 0 0 | |
| 144 chr1 8 12 2 1,3 1 0 1 | |
| 145 chr1 12 15 3 1,2,3 1 1 1 | |
| 146 chr1 15 20 2 1,2 1 1 0 | |
| 147 chr1 20 22 1 2 0 1 0 | |
| 148 chr1 22 30 2 1,2 1 1 0 | |
| 149 chr1 30 32 1 2 0 1 0 | |
| 150 chr1 32 34 1 3 0 0 1 | |
| 151 | |
| 152 | |
| 153 **Example adding a header line**:: | |
| 154 | |
| 155 | |
| 156 chrom start end num list a.bed b.bed c.bed | |
| 157 chr1 6 8 1 1 1 0 0 | |
| 158 chr1 8 12 2 1,3 1 0 1 | |
| 159 chr1 12 15 3 1,2,3 1 1 1 | |
| 160 chr1 15 20 2 1,2 1 1 0 | |
| 161 chr1 20 22 1 2 0 1 0 | |
| 162 chr1 22 30 2 1,2 1 1 0 | |
| 163 chr1 30 32 1 2 0 1 0 | |
| 164 chr1 32 34 1 3 0 0 1 | |
| 165 | |
| 166 | |
| 167 **Example adding a header line and custom file labels**:: | |
| 168 | |
| 169 | |
| 170 chrom start end num list joe bob sue | |
| 171 chr1 6 8 1 joe 1 0 0 | |
| 172 chr1 8 12 2 joe,sue 1 0 1 | |
| 173 chr1 12 15 3 joe,bob,sue 1 1 1 | |
| 174 chr1 15 20 2 joe,bob 1 1 0 | |
| 175 chr1 20 22 1 bob 0 1 0 | |
| 176 chr1 22 30 2 joe,bob 1 1 0 | |
| 177 chr1 30 32 1 bob 0 1 0 | |
| 178 chr1 32 34 1 sue 0 0 1 | |
| 179 | |
| 180 | |
| 181 @REFERENCES@ | |
| 182 ]]> | |
| 183 </help> | |
| 184 <expand macro="citations" /> | |
| 185 </tool> |