Mercurial > repos > iuc > bedtools
annotate genomeCoverageBed.xml @ 42:d279800f4ff9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
| author | iuc |
|---|---|
| date | Thu, 26 Apr 2018 17:02:24 -0400 |
| parents | ac2040a5e6ff |
| children | 2f457890d8c8 |
| rev | line source |
|---|---|
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ac2040a5e6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
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1 <tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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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 | |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
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11 @GENOME_FILE_COVERAGE@ |
| 8 | 12 |
| 13 $split | |
| 14 $strand | |
| 15 | |
| 16 #if str($report.report_select) == "bg": | |
| 17 #if $report.zero_regions: | |
| 18 $report.zero_regions | |
| 19 #else: | |
| 20 -bg | |
| 21 #end if | |
| 22 | |
| 23 #if str($report.scale): | |
| 24 -scale $report.scale | |
| 25 #end if | |
| 26 #else: | |
| 27 #if str($report.max): | |
| 28 -max $report.max | |
| 29 #end if | |
| 30 #end if | |
| 31 $d | |
| 32 $dz | |
| 33 $five | |
| 34 $three | |
| 35 | |
| 36 > '$output' | |
| 37 ]]> | |
| 38 </command> | |
| 39 <inputs> | |
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2a576a9ef0cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
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40 <conditional name="input_type"> |
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2a576a9ef0cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
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41 <param name="input_type_select" type="select" label="Input type"> |
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d279800f4ff9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
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42 <option value="bed">@STD_BEDTOOLS_INPUT_LABEL@</option> |
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2a576a9ef0cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
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43 <option value="bam">BAM</option> |
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2a576a9ef0cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
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44 </param> |
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2a576a9ef0cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
parents:
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changeset
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45 <when value="bed"> |
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42
d279800f4ff9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
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46 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" /> |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
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changeset
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47 <expand macro="input_conditional_genome_file" /> |
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2a576a9ef0cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
parents:
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48 </when> |
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2a576a9ef0cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
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49 <when value="bam"> |
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2a576a9ef0cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
parents:
20
diff
changeset
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50 <param format="bam" name="input" type="data" label="BAM file" /> |
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2a576a9ef0cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
parents:
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51 </when> |
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2a576a9ef0cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
parents:
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changeset
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52 </conditional> |
| 8 | 53 <conditional name="report"> |
| 54 <param name="report_select" type="select" label="Output type"> | |
| 55 <option value="bg" selected="true">BedGraph coverage file</option> | |
| 56 <option value="hist">Data suiteable for Histogram</option> | |
| 57 </param> | |
| 58 <when value="bg"> | |
| 59 <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue="" | |
| 60 label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported. (-bga)" /> | |
| 61 <param name="scale" type="float" value="1.0" | |
| 62 label="Scale the coverage by a constant factor" | |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
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diff
changeset
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63 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)" /> |
| 8 | 64 </when> |
| 65 <when value="hist"> | |
| 66 <param name="max" type="integer" label="Specify max depth" value="0" | |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
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diff
changeset
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67 help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)" /> |
| 8 | 68 </when> |
| 69 </conditional> | |
| 70 <expand macro="split" /> | |
| 71 <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)"> | |
| 72 <option value="">both strands combined</option> | |
| 73 <option value="-strand +">positive strand only</option> | |
| 74 <option value="-strand -">negative strand only</option> | |
| 75 </param> | |
| 76 | |
| 77 <param name="d" type="boolean" checked="False" truevalue="-d" falsevalue="" | |
| 78 label="Report the depth at each genome position with 1-based coordinates" help="(-d)" /> | |
| 79 <param name="dz" type="boolean" checked="False" truevalue="-dz" falsevalue="" | |
| 80 label="Report the depth at each genome position with 0-based coordinatess" help="(-dz)" /> | |
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3fe00810c5a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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81 <param name="five" type="boolean" checked="False" truevalue="-5" falsevalue="" |
| 8 | 82 label="Calculate coverage of 5’ positions" help="Instead of entire interval. (-5)" /> |
| 83 <param name="three" type="boolean" checked="False" truevalue="-3" falsevalue="" | |
| 84 label="Calculate coverage of 3’ positions" help="Instead of entire interval. (-3)" /> | |
| 85 </inputs> | |
| 86 <outputs> | |
| 87 <data format="bedgraph" name="output"> | |
| 88 <change_format> | |
| 89 <when input="report.report_select" value="hist" format="tabular" /> | |
| 90 </change_format> | |
| 91 </data> | |
| 92 </outputs> | |
| 93 <tests> | |
| 94 <test> | |
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2a576a9ef0cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
parents:
20
diff
changeset
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95 <param name="input_type_select" value="bed" /> |
| 8 | 96 <param name="input" value="genomeCoverageBed1.bed" ftype="bed" /> |
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b0d5e752c0c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
iuc
parents:
26
diff
changeset
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97 <param name="genome_file_opts_selector" value="hist" /> |
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2a576a9ef0cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
parents:
20
diff
changeset
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98 <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" /> |
| 8 | 99 <param name="report_select" value="hist" /> |
| 100 <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" /> | |
| 101 </test> | |
| 102 </tests> | |
| 103 <help> | |
| 104 <![CDATA[ | |
| 105 **What it does** | |
| 106 | |
| 107 This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format. | |
| 108 | |
| 109 .. image:: $PATH_TO_IMAGES/genomecov-glyph.png | |
| 110 | |
| 111 .. class:: warningmark | |
| 112 | |
| 113 The input BED or BAM file must be sorted by chromosome name (but doesn't necessarily have to be sorted by start position). | |
| 114 | |
| 115 ----- | |
| 116 | |
| 117 **Example 1** | |
| 118 | |
| 119 Input (BED format)- | |
| 120 Overlapping, un-sorted intervals:: | |
| 121 | |
| 122 chr1 140 176 | |
| 123 chr1 100 130 | |
| 124 chr1 120 147 | |
| 125 | |
| 126 | |
| 127 Output (BedGraph format)- | |
| 128 Sorted, non-overlapping intervals, with coverage value on the 4th column:: | |
| 129 | |
| 130 chr1 100 120 1 | |
| 131 chr1 120 130 2 | |
| 132 chr1 130 140 1 | |
| 133 chr1 140 147 2 | |
| 134 chr1 147 176 1 | |
| 135 | |
| 136 ----- | |
| 137 | |
| 138 **Example 2 - with ZERO-Regions selected (assuming hg19)** | |
| 139 | |
| 140 Input (BED format)- | |
| 141 Overlapping, un-sorted intervals:: | |
| 142 | |
| 143 chr1 140 176 | |
| 144 chr1 100 130 | |
| 145 chr1 120 147 | |
| 146 | |
| 147 | |
| 148 BedGraph output will contain five columns: | |
| 149 | |
| 150 * 1. Chromosome name (or 'genome' for whole-genome coverage) | |
| 151 * 2. Coverage depth | |
| 152 * 3. The number of bases on chromosome (or genome) with depth equal to column 2. | |
| 153 * 4. The size of chromosome (or entire genome) in base pairs | |
| 154 * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2. | |
| 155 | |
| 156 **Example Output**: | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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157 |
| 8 | 158 chr2L 0 1379895 23011544 0.0599653 |
| 159 chr2L 1 837250 23011544 0.0363839 | |
| 160 chr2L 2 904442 23011544 0.0393038 | |
| 161 chr2L 3 913723 23011544 0.0397072 | |
| 162 chr2L 4 952166 23011544 0.0413778 | |
| 163 chr2L 5 967763 23011544 0.0420555 | |
| 164 chr2L 6 986331 23011544 0.0428624 | |
| 165 chr2L 7 998244 23011544 0.0433801 | |
| 166 chr2L 8 995791 23011544 0.0432735 | |
| 167 chr2L 9 996398 23011544 0.0432999 | |
| 168 | |
| 169 | |
| 170 @REFERENCES@ | |
| 171 ]]> | |
| 172 </help> | |
| 173 <expand macro="citations" /> | |
| 174 </tool> |