Mercurial > repos > iuc > bedtools
annotate multiIntersectBed.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 |
| rev | line source |
|---|---|
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17
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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11
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changeset
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1 <tool id="bedtools_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.1"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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2 <description>identifies common intervals among multiple interval files</description> |
| 0 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 1 | 9 <![CDATA[ |
| 10 bedtools multiinter | |
| 0 | 11 $header |
| 1 | 12 $cluster |
| 13 -filler "${filler}" | |
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17
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
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14 $empty.empty_selector |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
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15 @GENOME_FILE_UNION@ |
| 0 | 16 |
| 1 | 17 #if str($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 | |
| 0 | 29 #end if |
| 30 | |
| 1 | 31 > '$output' |
| 32 ]]> | |
| 0 | 33 </command> |
| 34 <inputs> | |
| 1 | 35 <conditional name="tag"> |
| 36 <param name="tag_select" type="select" label="Sample name"> | |
| 0 | 37 <option value="tag" selected="true">Use input's tag</option> |
| 1 | 38 <option value="custom">Enter custom name per file</option> |
| 0 | 39 </param> |
| 40 <when value="tag"> | |
| 1 | 41 <param name="inputs" format="bed" type="data" multiple="True" label="BED files" /> |
| 0 | 42 </when> |
| 43 <when value="custom"> | |
| 1 | 44 <repeat name="beds" title="Add BED files" min="2" > |
| 45 <param name="input" format="bed" type="data" multiple="True" label="BED file" /> | |
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17
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
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46 <param name="custom_name" type="text" area="false" label="Custom sample name" /> |
| 1 | 47 </repeat> |
| 0 | 48 </when> |
| 49 </conditional> | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
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50 <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue="" |
| 1 | 51 label="Invoke Ryan Layers's clustering algorithm" |
| 52 help="(-cluster)" /> | |
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17
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
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53 <conditional name="empty"> |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
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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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
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diff
changeset
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55 <option value="-empty">Yes</option> |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
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56 <option value="">No</option> |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
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57 </param> |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
58 <when value="-empty"> |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
59 <expand macro="input_conditional_genome_file" /> |
|
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
60 </when> |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
61 <when value="" /> |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
62 </conditional> |
| 1 | 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" /> | |
| 0 | 67 |
| 68 </inputs> | |
| 69 <outputs> | |
| 1 | 70 <data format="bed" name="output" /> |
| 0 | 71 </outputs> |
| 1 | 72 <tests> |
| 73 <test> | |
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17
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
74 <param name="tag_select" value="tag" /> |
| 1 | 75 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> |
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17
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
76 <param name="empty_selector" value="" /> |
| 1 | 77 <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" /> |
| 78 </test> | |
| 79 <test> | |
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17
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
80 <param name="tag_select" value="tag" /> |
| 1 | 81 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> |
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17
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
82 <param name="header" value="True" /> |
|
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
83 <param name="empty_selector" value="" /> |
| 1 | 84 <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" /> |
| 85 </test> | |
| 86 <test> | |
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17
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
87 <param name="tag_select" value="tag" /> |
| 1 | 88 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> |
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17
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
89 <param name="empty_selector" value="-empty" /> |
|
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
90 <param name="genome_file_opts_selector" value="hist" /> |
|
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
diff
changeset
|
91 <param name="genome" value="multiIntersectBed1.len" /> |
| 1 | 92 <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" /> |
| 93 </test> | |
| 94 </tests> | |
| 0 | 95 <help> |
| 1 | 96 <![CDATA[ |
| 0 | 97 **What it does** |
| 98 | |
| 1 | 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. |
| 0 | 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 | |
| 1 | 123 chr1 6 12bed |
| 0 | 124 chr1 10 20 |
| 125 chr1 22 27 | |
| 126 chr1 24 30 | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
127 |
| 0 | 128 # b.bed |
| 129 chr1 12 32 | |
| 130 chr1 14 30 | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
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131 |
| 0 | 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@ | |
| 1 | 182 ]]> |
| 0 | 183 </help> |
| 184 <expand macro="citations" /> | |
| 185 </tool> |