Mercurial > repos > iuc > bedtools
annotate multiIntersectBed.xml @ 4:607c0576c6ab draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
| author | iuc |
|---|---|
| date | Wed, 27 Jan 2016 15:15:59 -0500 |
| parents | 82aac94b06c3 |
| children | 7308cc546a36 |
| rev | line source |
|---|---|
|
4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
diff
changeset
|
1 <tool id="bedtools_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.0"> |
|
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
diff
changeset
|
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}" | |
| 0 | 14 #if $zero.value == True: |
| 15 -empty | |
| 1 | 16 -g $genome |
| 0 | 17 #end if |
| 18 | |
| 1 | 19 #if str($tag.tag_select) == "tag": |
| 20 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] ) | |
| 21 -i "${files}" | |
| 22 #else: | |
| 23 -i | |
| 24 #for $file in $tag.beds: | |
| 25 "${file.input}" | |
| 26 #end for | |
| 27 -names | |
| 28 #for $file in $tag.beds: | |
| 29 "{$file.custom_name}" | |
| 30 #end for | |
| 0 | 31 #end if |
| 32 | |
| 1 | 33 > '$output' |
| 34 ]]> | |
| 0 | 35 </command> |
| 36 <inputs> | |
| 1 | 37 <conditional name="tag"> |
| 38 <param name="tag_select" type="select" label="Sample name"> | |
| 0 | 39 <option value="tag" selected="true">Use input's tag</option> |
| 1 | 40 <option value="custom">Enter custom name per file</option> |
| 0 | 41 </param> |
| 42 <when value="tag"> | |
| 1 | 43 <param name="inputs" format="bed" type="data" multiple="True" label="BED files" /> |
| 0 | 44 </when> |
| 45 <when value="custom"> | |
| 1 | 46 <repeat name="beds" title="Add BED files" min="2" > |
| 47 <param name="input" format="bed" type="data" multiple="True" label="BED file" /> | |
| 48 <param name="custom_name" type="text" area="false" label="Custom sample name"/> | |
| 49 </repeat> | |
| 0 | 50 </when> |
| 51 </conditional> | |
| 1 | 52 <expand macro="genome" /> |
| 53 <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue="" | |
| 54 label="Invoke Ryan Layers's clustering algorithm" | |
| 55 help="(-cluster)" /> | |
| 56 <param name="zero" type="boolean" checked="true" | |
| 57 label="Report regions that are not covered by any of the files" | |
| 58 help="If set, regions that are not overlapped by any file will also be reported. Requires a valid organism key for all input datasets" /> | |
| 59 <param name="filler" type="text" value="N/A" | |
| 60 label="Text to use for no-coverage value" | |
| 61 help="Can be 0.0, N/A, - or any other value. (-filler)" /> | |
| 62 <expand macro="print_header" /> | |
| 0 | 63 |
| 64 </inputs> | |
| 65 <outputs> | |
| 1 | 66 <data format="bed" name="output" /> |
| 0 | 67 </outputs> |
| 1 | 68 <tests> |
| 69 <test> | |
| 70 <param name="tag_select" value="tag"/> | |
| 71 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> | |
| 72 <param name="zero" value="False"/> | |
| 73 <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" /> | |
| 74 </test> | |
| 75 <test> | |
| 76 <param name="tag_select" value="tag"/> | |
| 77 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> | |
| 78 <param name="header" value="True"/> | |
| 79 <param name="zero" value="False"/> | |
| 80 <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" /> | |
| 81 </test> | |
| 82 <test> | |
| 83 <param name="tag_select" value="tag"/> | |
| 84 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" /> | |
| 85 <param name="zero" value="True"/> | |
| 86 <param name="genome" value="multiIntersectBed1.len"/> | |
| 87 <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" /> | |
| 88 </test> | |
| 89 </tests> | |
| 0 | 90 <help> |
| 1 | 91 <![CDATA[ |
| 0 | 92 **What it does** |
| 93 | |
| 1 | 94 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 | 95 |
| 96 | |
| 97 .. class:: warningmark | |
| 98 | |
| 99 This tool requires that each BED file is reference-sorted (chrom, then start). | |
| 100 | |
| 101 | |
| 102 .. class:: infomark | |
| 103 | |
| 104 The output file will contain five fixed columns, plus additional columns for each BED file: | |
| 105 | |
| 106 * 1. Chromosome name (or 'genome' for whole-genome coverage). | |
| 107 * 2. The zero-based start position of the interval. | |
| 108 * 3. The one-based end position of the interval. | |
| 109 * 4. The number of input files that had at least one feature overlapping this interval. | |
| 110 * 5. A list of input files or labels that had at least one feature overlapping this interval. | |
| 111 * 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. | |
| 112 | |
| 113 ------ | |
| 114 | |
| 115 **Example input**:: | |
| 116 | |
| 117 # a.bed | |
| 1 | 118 chr1 6 12bed |
| 0 | 119 chr1 10 20 |
| 120 chr1 22 27 | |
| 121 chr1 24 30 | |
| 122 | |
| 123 # b.bed | |
| 124 chr1 12 32 | |
| 125 chr1 14 30 | |
| 126 | |
| 127 # c.bed | |
| 128 chr1 8 15 | |
| 129 chr1 10 14 | |
| 130 chr1 32 34 | |
| 131 | |
| 132 | |
| 133 ------ | |
| 134 | |
| 135 **Example without a header and without reporting intervals with zero coverage**:: | |
| 136 | |
| 137 | |
| 138 chr1 6 8 1 1 1 0 0 | |
| 139 chr1 8 12 2 1,3 1 0 1 | |
| 140 chr1 12 15 3 1,2,3 1 1 1 | |
| 141 chr1 15 20 2 1,2 1 1 0 | |
| 142 chr1 20 22 1 2 0 1 0 | |
| 143 chr1 22 30 2 1,2 1 1 0 | |
| 144 chr1 30 32 1 2 0 1 0 | |
| 145 chr1 32 34 1 3 0 0 1 | |
| 146 | |
| 147 | |
| 148 **Example adding a header line**:: | |
| 149 | |
| 150 | |
| 151 chrom start end num list a.bed b.bed c.bed | |
| 152 chr1 6 8 1 1 1 0 0 | |
| 153 chr1 8 12 2 1,3 1 0 1 | |
| 154 chr1 12 15 3 1,2,3 1 1 1 | |
| 155 chr1 15 20 2 1,2 1 1 0 | |
| 156 chr1 20 22 1 2 0 1 0 | |
| 157 chr1 22 30 2 1,2 1 1 0 | |
| 158 chr1 30 32 1 2 0 1 0 | |
| 159 chr1 32 34 1 3 0 0 1 | |
| 160 | |
| 161 | |
| 162 **Example adding a header line and custom file labels**:: | |
| 163 | |
| 164 | |
| 165 chrom start end num list joe bob sue | |
| 166 chr1 6 8 1 joe 1 0 0 | |
| 167 chr1 8 12 2 joe,sue 1 0 1 | |
| 168 chr1 12 15 3 joe,bob,sue 1 1 1 | |
| 169 chr1 15 20 2 joe,bob 1 1 0 | |
| 170 chr1 20 22 1 bob 0 1 0 | |
| 171 chr1 22 30 2 joe,bob 1 1 0 | |
| 172 chr1 30 32 1 bob 0 1 0 | |
| 173 chr1 32 34 1 sue 0 0 1 | |
| 174 | |
| 175 | |
| 176 @REFERENCES@ | |
| 1 | 177 ]]> |
| 0 | 178 </help> |
| 179 <expand macro="citations" /> | |
| 180 </tool> |