Mercurial > repos > iuc > bedtools
annotate genomeCoverageBed.xml @ 17:a2d4c30ba2f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
| author | iuc |
|---|---|
| date | Sun, 21 Jun 2015 22:49:46 -0400 |
| parents | 0d3aa592ce27 |
| children | 3fe00810c5a2 |
| rev | line source |
|---|---|
| 8 | 1 <tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0"> |
|
17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
|
2 <description>compute the coverage over an entire genome</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 genomecov | |
| 11 #if $input.ext == "bam" | |
| 12 -ibam '$input' | |
| 13 #else | |
| 14 -i '$input' | |
| 15 -g $genome | |
| 16 #end if | |
| 17 | |
| 18 $split | |
| 19 $strand | |
| 20 | |
| 21 #if str($report.report_select) == "bg": | |
| 22 #if $report.zero_regions: | |
| 23 $report.zero_regions | |
| 24 #else: | |
| 25 -bg | |
| 26 #end if | |
| 27 | |
| 28 #if str($report.scale): | |
| 29 -scale $report.scale | |
| 30 #end if | |
| 31 #else: | |
| 32 #if str($report.max): | |
| 33 -max $report.max | |
| 34 #end if | |
| 35 #end if | |
| 36 $d | |
| 37 $dz | |
| 38 $five | |
| 39 $three | |
| 40 | |
| 41 > '$output' | |
| 42 ]]> | |
| 43 </command> | |
| 44 <inputs> | |
| 45 <param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed"> | |
| 46 <validator type="unspecified_build" /> | |
| 47 </param> | |
| 48 <conditional name="report"> | |
| 49 <param name="report_select" type="select" label="Output type"> | |
| 50 <option value="bg" selected="true">BedGraph coverage file</option> | |
| 51 <option value="hist">Data suiteable for Histogram</option> | |
| 52 </param> | |
| 53 <when value="bg"> | |
| 54 <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue="" | |
| 55 label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported. (-bga)" /> | |
| 56 <param name="scale" type="float" value="1.0" | |
| 57 label="Scale the coverage by a constant factor" | |
| 58 help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)"/> | |
| 59 </when> | |
| 60 <when value="hist"> | |
| 61 <param name="max" type="integer" label="Specify max depth" value="0" | |
| 62 help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)"/> | |
| 63 </when> | |
| 64 </conditional> | |
| 65 <expand macro="genome" /> | |
| 66 <expand macro="split" /> | |
| 67 <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)"> | |
| 68 <option value="">both strands combined</option> | |
| 69 <option value="-strand +">positive strand only</option> | |
| 70 <option value="-strand -">negative strand only</option> | |
| 71 </param> | |
| 72 | |
| 73 <param name="d" type="boolean" checked="False" truevalue="-d" falsevalue="" | |
| 74 label="Report the depth at each genome position with 1-based coordinates" help="(-d)" /> | |
| 75 <param name="dz" type="boolean" checked="False" truevalue="-dz" falsevalue="" | |
| 76 label="Report the depth at each genome position with 0-based coordinatess" help="(-dz)" /> | |
| 77 <param name="five" type="boolean" checked="False" truevalue="-d" falsevalue="" | |
| 78 label="Calculate coverage of 5’ positions" help="Instead of entire interval. (-5)" /> | |
| 79 <param name="three" type="boolean" checked="False" truevalue="-3" falsevalue="" | |
| 80 label="Calculate coverage of 3’ positions" help="Instead of entire interval. (-3)" /> | |
| 81 </inputs> | |
| 82 <outputs> | |
| 83 <data format="bedgraph" name="output"> | |
| 84 <change_format> | |
| 85 <when input="report.report_select" value="hist" format="tabular" /> | |
| 86 </change_format> | |
| 87 </data> | |
| 88 </outputs> | |
| 89 <tests> | |
| 90 <test> | |
| 91 <param name="input" value="genomeCoverageBed1.bed" ftype="bed" /> | |
| 92 <param name="genome" value="genomeCoverageBed1.len" /> | |
| 93 <param name="report_select" value="hist" /> | |
| 94 <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" /> | |
| 95 </test> | |
| 96 </tests> | |
| 97 <help> | |
| 98 <![CDATA[ | |
| 99 **What it does** | |
| 100 | |
| 101 This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format. | |
| 102 | |
| 103 .. image:: $PATH_TO_IMAGES/genomecov-glyph.png | |
| 104 | |
| 105 .. class:: warningmark | |
| 106 | |
| 107 The input BED or BAM file must be sorted by chromosome name (but doesn't necessarily have to be sorted by start position). | |
| 108 | |
| 109 ----- | |
| 110 | |
| 111 **Example 1** | |
| 112 | |
| 113 Input (BED format)- | |
| 114 Overlapping, un-sorted intervals:: | |
| 115 | |
| 116 chr1 140 176 | |
| 117 chr1 100 130 | |
| 118 chr1 120 147 | |
| 119 | |
| 120 | |
| 121 Output (BedGraph format)- | |
| 122 Sorted, non-overlapping intervals, with coverage value on the 4th column:: | |
| 123 | |
| 124 chr1 100 120 1 | |
| 125 chr1 120 130 2 | |
| 126 chr1 130 140 1 | |
| 127 chr1 140 147 2 | |
| 128 chr1 147 176 1 | |
| 129 | |
| 130 ----- | |
| 131 | |
| 132 **Example 2 - with ZERO-Regions selected (assuming hg19)** | |
| 133 | |
| 134 Input (BED format)- | |
| 135 Overlapping, un-sorted intervals:: | |
| 136 | |
| 137 chr1 140 176 | |
| 138 chr1 100 130 | |
| 139 chr1 120 147 | |
| 140 | |
| 141 | |
| 142 BedGraph output will contain five columns: | |
| 143 | |
| 144 * 1. Chromosome name (or 'genome' for whole-genome coverage) | |
| 145 * 2. Coverage depth | |
| 146 * 3. The number of bases on chromosome (or genome) with depth equal to column 2. | |
| 147 * 4. The size of chromosome (or entire genome) in base pairs | |
| 148 * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2. | |
| 149 | |
| 150 **Example Output**: | |
| 151 | |
| 152 chr2L 0 1379895 23011544 0.0599653 | |
| 153 chr2L 1 837250 23011544 0.0363839 | |
| 154 chr2L 2 904442 23011544 0.0393038 | |
| 155 chr2L 3 913723 23011544 0.0397072 | |
| 156 chr2L 4 952166 23011544 0.0413778 | |
| 157 chr2L 5 967763 23011544 0.0420555 | |
| 158 chr2L 6 986331 23011544 0.0428624 | |
| 159 chr2L 7 998244 23011544 0.0433801 | |
| 160 chr2L 8 995791 23011544 0.0432735 | |
| 161 chr2L 9 996398 23011544 0.0432999 | |
| 162 | |
| 163 | |
| 164 @REFERENCES@ | |
| 165 ]]> | |
| 166 </help> | |
| 167 <expand macro="citations" /> | |
| 168 </tool> |