Mercurial > repos > iuc > bedtools
annotate unionBedGraphs.xml @ 29:6bb3cd018203 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 69394918e7a50dad3ae578e932cbac27b96e0d3b
| author | iuc |
|---|---|
| date | Tue, 24 Jul 2018 11:49:55 -0400 |
| parents | a8eabd2838f6 |
| children | 4f7a5ccd2ae9 |
| rev | line source |
|---|---|
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a8eabd2838f6
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_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0"> |
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4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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2 <description>combines coverage intervals from multiple BEDGRAPH files</description> |
| 0 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 1 | 8 <command> |
| 9 <![CDATA[ | |
| 10 unionBedGraphs | |
| 0 | 11 $header |
| 1 | 12 -filler "${filler}" |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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13 $empty.empty_selector |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
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14 @GENOME_FILE_UNION@ |
| 0 | 15 |
| 1 | 16 #if str($tag.tag_select) == "tag": |
| 17 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] ) | |
| 18 -i "${files}" | |
| 19 #else: | |
| 20 -i | |
| 21 #for $bg in $tag.bedgraphs: | |
| 22 "${bg.input}" | |
| 23 #end for | |
| 24 -names | |
| 25 #for $bg in $tag.bedgraphs: | |
| 26 "${bg.custom_name}" | |
| 27 #end for | |
| 0 | 28 #end if |
| 1 | 29 > "${output}" |
| 30 ]]> | |
| 0 | 31 </command> |
| 32 <inputs> | |
| 1 | 33 <conditional name="tag"> |
| 34 <param name="tag_select" type="select" label="Sample name"> | |
| 0 | 35 <option value="tag" selected="true">Use input's tag</option> |
| 1 | 36 <option value="custom">Enter custom name per file</option> |
| 0 | 37 </param> |
| 38 <when value="tag"> | |
| 1 | 39 <param name="inputs" format="bedgraph" type="data" multiple="True" label="BedGraph files" /> |
| 0 | 40 </when> |
| 41 <when value="custom"> | |
| 1 | 42 <repeat name="bedgraphs" title="Add BedGraph files" min="2" > |
| 43 <param name="input" format="bedgraph" type="data" multiple="True" label="BedGraph file" /> | |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
11
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changeset
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44 <param name="custom_name" type="text" area="false" label="Custom sample name" /> |
| 1 | 45 </repeat> |
| 0 | 46 </when> |
| 47 </conditional> | |
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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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48 <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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49 <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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50 <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
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51 <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
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52 </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
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53 <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
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54 <expand macro="input_conditional_genome_file" /> |
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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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55 </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
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56 <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
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changeset
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57 </conditional> |
| 1 | 58 <param name="filler" type="text" value="N/A" |
| 59 label="Text to use for no-coverage value" | |
| 60 help="Can be 0.0, N/A, - or any other value. (-filler)" /> | |
| 61 <expand macro="print_header" /> | |
| 0 | 62 </inputs> |
| 63 <outputs> | |
| 1 | 64 <data name="output" format="bedgraph" /> |
| 0 | 65 </outputs> |
| 1 | 66 <tests> |
| 67 <test> | |
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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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68 <param name="tag_select" value="tag" /> |
| 1 | 69 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> |
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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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70 <param name="empty_selector" value="" /> |
| 1 | 71 <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" /> |
| 72 </test> | |
| 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
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74 <param name="tag_select" value="tag" /> |
| 1 | 75 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> |
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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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76 <param name="header" value="True" /> |
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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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77 <param name="empty_selector" value="" /> |
| 1 | 78 <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" /> |
| 79 </test> | |
| 80 <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
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81 <param name="tag_select" value="tag" /> |
| 1 | 82 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> |
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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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83 <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
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84 <param name="genome_file_opts_selector" value="hist" /> |
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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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85 <param name="genome" value="unionBedGraphs1.len" /> |
| 1 | 86 <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" /> |
| 87 </test> | |
| 88 <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
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89 <param name="tag_select" value="custom" /> |
| 1 | 90 <repeat name="bedgraphs"> |
| 91 <param name="input" value="unionBedGraphs1.bg" /> | |
| 92 <param name="custom_name" value="first" /> | |
| 93 </repeat> | |
| 94 <repeat name="bedgraphs"> | |
| 95 <param name="input" value="unionBedGraphs2.bg" /> | |
| 96 <param name="custom_name" value="second" /> | |
| 97 </repeat> | |
| 98 <repeat name="bedgraphs"> | |
| 99 <param name="input" value="unionBedGraphs3.bg" /> | |
| 100 <param name="custom_name" value="third" /> | |
| 101 </repeat> | |
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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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102 <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
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103 <param name="genome_file_opts_selector" value="hist" /> |
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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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104 <param name="genome" value="unionBedGraphs1.len" /> |
| 1 | 105 <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" /> |
| 106 </test> | |
| 107 </tests> | |
| 0 | 108 <help> |
| 1 | 109 <![CDATA[ |
| 0 | 110 **What it does** |
| 111 | |
| 112 This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files. | |
| 113 | |
| 114 .. class:: warningmark | |
| 115 | |
| 116 This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file). | |
| 117 | |
| 118 | |
| 119 ------ | |
| 120 | |
| 121 **Example input**:: | |
| 122 | |
| 123 # 1.bedgraph | |
| 124 chr1 1000 1500 10 | |
| 125 chr1 2000 2100 20 | |
| 126 | |
| 127 # 2.bedgraph | |
| 128 chr1 900 1600 60 | |
| 129 chr1 1700 2050 50 | |
| 130 | |
| 131 # 3.bedgraph | |
| 132 chr1 1980 2070 80 | |
| 133 chr1 2090 2100 20 | |
| 134 | |
| 135 | |
| 136 ------ | |
| 137 | |
| 138 **Examples using the Zero Coverage checkbox** | |
| 139 | |
| 140 Output example (*without* checking "Report regions with zero coverage"):: | |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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141 |
| 0 | 142 chr1 900 1000 0 60 0 |
| 143 chr1 1000 1500 10 60 0 | |
| 144 chr1 1500 1600 0 60 0 | |
| 145 chr1 1700 1980 0 50 0 | |
| 146 chr1 1980 2000 0 50 80 | |
| 147 chr1 2000 2050 20 50 80 | |
| 148 chr1 2050 2070 20 0 80 | |
| 149 chr1 2070 2090 20 0 0 | |
| 150 chr1 2090 2100 20 0 20 | |
| 151 | |
| 152 | |
| 153 Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).:: | |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
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changeset
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154 |
| 0 | 155 chr1 0 900 0 0 0 (*) |
| 156 chr1 900 1000 0 60 0 | |
| 157 chr1 1000 1500 10 60 0 | |
| 158 chr1 1500 1600 0 60 0 | |
| 159 chr1 1600 1700 0 0 0 (*) | |
| 160 chr1 1700 1980 0 50 0 | |
| 161 chr1 1980 2000 0 50 80 | |
| 162 chr1 2000 2050 20 50 80 | |
| 163 chr1 2050 2070 20 0 80 | |
| 164 chr1 2070 2090 20 0 0 | |
| 165 chr1 2090 2100 20 0 20 | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
10
diff
changeset
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166 chr1 2100 247249719 0 0 0 (*) |
| 0 | 167 |
| 168 | |
| 169 ------ | |
| 170 | |
| 171 **Examples adjusting the "Filler value" for no-covered intervals** | |
| 172 | |
| 173 The default value is '0', but you can use any other value. | |
| 174 | |
| 175 Output example with **filler = N/A**:: | |
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7308cc546a36
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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176 |
| 0 | 177 chr1 900 1000 N/A 60 N/A |
| 178 chr1 1000 1500 10 60 N/A | |
| 179 chr1 1500 1600 N/A 60 N/A | |
| 180 chr1 1600 1700 N/A N/A N/A | |
| 181 chr1 1700 1980 N/A 50 N/A | |
| 182 chr1 1980 2000 N/A 50 80 | |
| 183 chr1 2000 2050 20 50 80 | |
| 184 chr1 2050 2070 20 N/A 80 | |
| 185 chr1 2070 2090 20 N/A N/A | |
| 186 chr1 2090 2100 20 N/A 20 | |
| 187 | |
| 188 | |
| 189 ------ | |
| 190 | |
| 191 **Examples using the "sample name" labels**:: | |
| 192 | |
| 193 chrom start end WT-1 WT-2 KO-1 | |
| 194 chr1 900 1000 N/A 60 N/A | |
| 195 chr1 1000 1500 10 60 N/A | |
| 196 chr1 1500 1600 N/A 60 N/A | |
| 197 chr1 1600 1700 N/A N/A N/A | |
| 198 chr1 1700 1980 N/A 50 N/A | |
| 199 chr1 1980 2000 N/A 50 80 | |
| 200 chr1 2000 2050 20 50 80 | |
| 201 chr1 2050 2070 20 N/A 80 | |
| 202 chr1 2070 2090 20 N/A N/A | |
| 203 chr1 2090 2100 20 N/A 20 | |
| 204 | |
| 205 | |
| 206 ------ | |
| 207 | |
| 208 **Non-numeric values** | |
| 209 | |
| 210 The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value. | |
| 211 | |
| 212 Input Example:: | |
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7308cc546a36
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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213 |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
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changeset
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214 File-1 File-2 |
| 0 | 215 chr1 200 300 Sample1 chr1 100 240 0.75 |
| 216 chr1 400 450 Sample1 chr1 250 700 0.43 | |
| 217 chr1 530 600 Sample2 | |
| 218 | |
| 219 Output Example:: | |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
10
diff
changeset
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220 |
| 0 | 221 chr1 100 200 0 0.75 |
| 222 chr1 200 240 Sample1 0.75 | |
| 223 chr1 240 250 Sample1 0 | |
| 224 chr1 250 300 Sample1 0.43 | |
| 225 chr1 300 400 0 0.43 | |
| 226 chr1 400 450 Sample1 0.43 | |
| 227 chr1 450 530 0 0.43 | |
| 228 chr1 530 600 Sample2 0.43 | |
| 229 chr1 600 700 0 0.43 | |
| 230 | |
| 231 @REFERENCES@ | |
| 1 | 232 ]]> |
| 0 | 233 </help> |
| 234 <expand macro="citations" /> | |
| 235 </tool> |