Mercurial > repos > iuc > bedtools
annotate unionBedGraphs.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 | c78cf6fe3018 |
| rev | line source |
|---|---|
| 1 | 1 <tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0"> |
|
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}" |
| 0 | 13 #if $zero.value == True: |
| 14 -empty | |
| 1 | 15 -g $genome |
| 0 | 16 #end if |
| 17 | |
| 1 | 18 #if str($tag.tag_select) == "tag": |
| 19 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] ) | |
| 20 -i "${files}" | |
| 21 #else: | |
| 22 -i | |
| 23 #for $bg in $tag.bedgraphs: | |
| 24 "${bg.input}" | |
| 25 #end for | |
| 26 -names | |
| 27 #for $bg in $tag.bedgraphs: | |
| 28 "${bg.custom_name}" | |
| 29 #end for | |
| 0 | 30 #end if |
| 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="bedgraph" type="data" multiple="True" label="BedGraph files" /> |
| 0 | 42 </when> |
| 43 <when value="custom"> | |
| 1 | 44 <repeat name="bedgraphs" title="Add BedGraph files" min="2" > |
| 45 <param name="input" format="bedgraph" type="data" multiple="True" label="BedGraph file" /> | |
| 46 <param name="custom_name" type="text" area="false" label="Custom sample name"/> | |
| 47 </repeat> | |
| 0 | 48 </when> |
| 49 </conditional> | |
| 1 | 50 <expand macro="genome" /> |
| 51 <param name="zero" type="boolean" checked="true" | |
| 52 label="Report regions with zero coverage" | |
| 53 help="If set, regions without any coverage will also be reported. Requires a valid organism key for all input datasets" /> | |
| 54 <param name="filler" type="text" value="N/A" | |
| 55 label="Text to use for no-coverage value" | |
| 56 help="Can be 0.0, N/A, - or any other value. (-filler)" /> | |
| 57 <expand macro="print_header" /> | |
| 0 | 58 </inputs> |
| 59 <outputs> | |
| 1 | 60 <data name="output" format="bedgraph" /> |
| 0 | 61 </outputs> |
| 1 | 62 <tests> |
| 63 <test> | |
| 64 <param name="tag_select" value="tag"/> | |
| 65 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> | |
| 66 <param name="zero" value="False"/> | |
| 67 <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" /> | |
| 68 </test> | |
| 69 <test> | |
| 70 <param name="tag_select" value="tag"/> | |
| 71 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> | |
| 72 <param name="header" value="True"/> | |
| 73 <param name="zero" value="False"/> | |
| 74 <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" /> | |
| 75 </test> | |
| 76 <test> | |
| 77 <param name="tag_select" value="tag"/> | |
| 78 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> | |
| 79 <param name="zero" value="True"/> | |
| 80 <param name="genome" value="unionBedGraphs1.len"/> | |
| 81 <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" /> | |
| 82 </test> | |
| 83 <test> | |
| 84 <param name="tag_select" value="custom"/> | |
| 85 <repeat name="bedgraphs"> | |
| 86 <param name="input" value="unionBedGraphs1.bg" /> | |
| 87 <param name="custom_name" value="first" /> | |
| 88 </repeat> | |
| 89 <repeat name="bedgraphs"> | |
| 90 <param name="input" value="unionBedGraphs2.bg" /> | |
| 91 <param name="custom_name" value="second" /> | |
| 92 </repeat> | |
| 93 <repeat name="bedgraphs"> | |
| 94 <param name="input" value="unionBedGraphs3.bg" /> | |
| 95 <param name="custom_name" value="third" /> | |
| 96 </repeat> | |
| 97 <param name="zero" value="True"/> | |
| 98 <param name="genome" value="unionBedGraphs1.len"/> | |
| 99 <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" /> | |
| 100 </test> | |
| 101 </tests> | |
| 0 | 102 <help> |
| 1 | 103 <![CDATA[ |
| 0 | 104 **What it does** |
| 105 | |
| 106 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. | |
| 107 | |
| 108 .. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/ubg.png | |
| 109 | |
| 110 | |
| 111 .. class:: warningmark | |
| 112 | |
| 113 This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file). | |
| 114 | |
| 115 | |
| 116 ------ | |
| 117 | |
| 118 **Example input**:: | |
| 119 | |
| 120 # 1.bedgraph | |
| 121 chr1 1000 1500 10 | |
| 122 chr1 2000 2100 20 | |
| 123 | |
| 124 # 2.bedgraph | |
| 125 chr1 900 1600 60 | |
| 126 chr1 1700 2050 50 | |
| 127 | |
| 128 # 3.bedgraph | |
| 129 chr1 1980 2070 80 | |
| 130 chr1 2090 2100 20 | |
| 131 | |
| 132 | |
| 133 ------ | |
| 134 | |
| 135 **Examples using the Zero Coverage checkbox** | |
| 136 | |
| 137 Output example (*without* checking "Report regions with zero coverage"):: | |
| 138 | |
| 139 chr1 900 1000 0 60 0 | |
| 140 chr1 1000 1500 10 60 0 | |
| 141 chr1 1500 1600 0 60 0 | |
| 142 chr1 1700 1980 0 50 0 | |
| 143 chr1 1980 2000 0 50 80 | |
| 144 chr1 2000 2050 20 50 80 | |
| 145 chr1 2050 2070 20 0 80 | |
| 146 chr1 2070 2090 20 0 0 | |
| 147 chr1 2090 2100 20 0 20 | |
| 148 | |
| 149 | |
| 150 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).:: | |
| 151 | |
| 152 chr1 0 900 0 0 0 (*) | |
| 153 chr1 900 1000 0 60 0 | |
| 154 chr1 1000 1500 10 60 0 | |
| 155 chr1 1500 1600 0 60 0 | |
| 156 chr1 1600 1700 0 0 0 (*) | |
| 157 chr1 1700 1980 0 50 0 | |
| 158 chr1 1980 2000 0 50 80 | |
| 159 chr1 2000 2050 20 50 80 | |
| 160 chr1 2050 2070 20 0 80 | |
| 161 chr1 2070 2090 20 0 0 | |
| 162 chr1 2090 2100 20 0 20 | |
| 163 chr1 2100 247249719 0 0 0 (*) | |
| 164 | |
| 165 | |
| 166 ------ | |
| 167 | |
| 168 **Examples adjusting the "Filler value" for no-covered intervals** | |
| 169 | |
| 170 The default value is '0', but you can use any other value. | |
| 171 | |
| 172 Output example with **filler = N/A**:: | |
| 173 | |
| 174 chr1 900 1000 N/A 60 N/A | |
| 175 chr1 1000 1500 10 60 N/A | |
| 176 chr1 1500 1600 N/A 60 N/A | |
| 177 chr1 1600 1700 N/A N/A N/A | |
| 178 chr1 1700 1980 N/A 50 N/A | |
| 179 chr1 1980 2000 N/A 50 80 | |
| 180 chr1 2000 2050 20 50 80 | |
| 181 chr1 2050 2070 20 N/A 80 | |
| 182 chr1 2070 2090 20 N/A N/A | |
| 183 chr1 2090 2100 20 N/A 20 | |
| 184 | |
| 185 | |
| 186 ------ | |
| 187 | |
| 188 **Examples using the "sample name" labels**:: | |
| 189 | |
| 190 chrom start end WT-1 WT-2 KO-1 | |
| 191 chr1 900 1000 N/A 60 N/A | |
| 192 chr1 1000 1500 10 60 N/A | |
| 193 chr1 1500 1600 N/A 60 N/A | |
| 194 chr1 1600 1700 N/A N/A N/A | |
| 195 chr1 1700 1980 N/A 50 N/A | |
| 196 chr1 1980 2000 N/A 50 80 | |
| 197 chr1 2000 2050 20 50 80 | |
| 198 chr1 2050 2070 20 N/A 80 | |
| 199 chr1 2070 2090 20 N/A N/A | |
| 200 chr1 2090 2100 20 N/A 20 | |
| 201 | |
| 202 | |
| 203 ------ | |
| 204 | |
| 205 **Non-numeric values** | |
| 206 | |
| 207 The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value. | |
| 208 | |
| 209 Input Example:: | |
| 210 | |
| 211 File-1 File-2 | |
| 212 chr1 200 300 Sample1 chr1 100 240 0.75 | |
| 213 chr1 400 450 Sample1 chr1 250 700 0.43 | |
| 214 chr1 530 600 Sample2 | |
| 215 | |
| 216 Output Example:: | |
| 217 | |
| 218 chr1 100 200 0 0.75 | |
| 219 chr1 200 240 Sample1 0.75 | |
| 220 chr1 240 250 Sample1 0 | |
| 221 chr1 250 300 Sample1 0.43 | |
| 222 chr1 300 400 0 0.43 | |
| 223 chr1 400 450 Sample1 0.43 | |
| 224 chr1 450 530 0 0.43 | |
| 225 chr1 530 600 Sample2 0.43 | |
| 226 chr1 600 700 0 0.43 | |
| 227 | |
| 228 @REFERENCES@ | |
| 1 | 229 ]]> |
| 0 | 230 </help> |
| 231 <expand macro="citations" /> | |
| 232 </tool> |