Mercurial > repos > iuc > bedtools
annotate genomeCoverageBed.xml @ 11:7308cc546a36 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
| author | iuc |
|---|---|
| date | Mon, 17 Oct 2016 10:13:35 -0400 |
| parents | 8e6b7c3597a8 |
| children | 44867b59dbf2 |
| rev | line source |
|---|---|
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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1 <tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
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2 <description>compute the coverage over an entire genome</description> |
| 1 | 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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8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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11 #if $input_type.input_type_select == 'bam' |
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8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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12 -ibam '$input_type.input' |
| 1 | 13 #else |
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8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
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14 -i '$input_type.input' |
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8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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15 -g '$input_type.genome' |
| 1 | 16 #end if |
| 17 | |
| 18 $split | |
| 19 $strand | |
| 20 | |
| 21 #if str($report.report_select) == "bg": | |
| 2 | 22 #if $report.zero_regions: |
| 23 $report.zero_regions | |
| 1 | 24 #else: |
| 25 -bg | |
| 26 #end if | |
| 27 | |
| 2 | 28 #if str($report.scale): |
| 29 -scale $report.scale | |
| 1 | 30 #end if |
| 31 #else: | |
| 32 #if str($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> | |
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8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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45 <conditional name="input_type"> |
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8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
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46 <param name="input_type_select" type="select" label="Input type"> |
|
8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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47 <option value="bed">BED/VCF/GFF</option> |
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8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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48 <option value="bam">BAM</option> |
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8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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49 </param> |
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8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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50 <when value="bed"> |
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8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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51 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" /> |
|
8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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52 <expand macro="genome" /> |
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8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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53 </when> |
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8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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54 <when value="bam"> |
|
8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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55 <param format="bam" name="input" type="data" label="BAM file" /> |
|
8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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56 </when> |
|
8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
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|
57 </conditional> |
| 1 | 58 <conditional name="report"> |
| 59 <param name="report_select" type="select" label="Output type"> | |
| 60 <option value="bg" selected="true">BedGraph coverage file</option> | |
| 61 <option value="hist">Data suiteable for Histogram</option> | |
| 62 </param> | |
| 63 <when value="bg"> | |
| 64 <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue="" | |
| 65 label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported. (-bga)" /> | |
| 66 <param name="scale" type="float" value="1.0" | |
| 67 label="Scale the coverage by a constant factor" | |
| 68 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)"/> | |
| 69 </when> | |
| 70 <when value="hist"> | |
| 71 <param name="max" type="integer" label="Specify max depth" value="0" | |
| 72 help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)"/> | |
| 73 </when> | |
| 74 </conditional> | |
| 75 <expand macro="split" /> | |
| 76 <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)"> | |
| 77 <option value="">both strands combined</option> | |
| 78 <option value="-strand +">positive strand only</option> | |
| 79 <option value="-strand -">negative strand only</option> | |
| 80 </param> | |
| 81 | |
| 82 <param name="d" type="boolean" checked="False" truevalue="-d" falsevalue="" | |
| 83 label="Report the depth at each genome position with 1-based coordinates" help="(-d)" /> | |
| 84 <param name="dz" type="boolean" checked="False" truevalue="-dz" falsevalue="" | |
| 85 label="Report the depth at each genome position with 0-based coordinatess" help="(-dz)" /> | |
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4
607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
2
diff
changeset
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86 <param name="five" type="boolean" checked="False" truevalue="-5" falsevalue="" |
| 1 | 87 label="Calculate coverage of 5’ positions" help="Instead of entire interval. (-5)" /> |
| 88 <param name="three" type="boolean" checked="False" truevalue="-3" falsevalue="" | |
| 89 label="Calculate coverage of 3’ positions" help="Instead of entire interval. (-3)" /> | |
| 90 </inputs> | |
| 91 <outputs> | |
| 92 <data format="bedgraph" name="output"> | |
| 93 <change_format> | |
| 94 <when input="report.report_select" value="hist" format="tabular" /> | |
| 95 </change_format> | |
| 96 </data> | |
| 97 </outputs> | |
| 98 <tests> | |
| 99 <test> | |
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7
8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
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changeset
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100 <param name="input_type_select" value="bed" /> |
| 1 | 101 <param name="input" value="genomeCoverageBed1.bed" ftype="bed" /> |
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7
8e6b7c3597a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
iuc
parents:
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diff
changeset
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102 <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" /> |
| 1 | 103 <param name="report_select" value="hist" /> |
| 104 <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" /> | |
| 105 </test> | |
| 106 </tests> | |
| 107 <help> | |
| 108 <![CDATA[ | |
| 109 **What it does** | |
| 110 | |
| 111 This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format. | |
| 112 | |
| 113 .. image:: $PATH_TO_IMAGES/genomecov-glyph.png | |
| 114 | |
| 115 .. class:: warningmark | |
| 116 | |
| 117 The input BED or BAM file must be sorted by chromosome name (but doesn't necessarily have to be sorted by start position). | |
| 118 | |
| 119 ----- | |
| 120 | |
| 121 **Example 1** | |
| 122 | |
| 123 Input (BED format)- | |
| 124 Overlapping, un-sorted intervals:: | |
| 125 | |
| 126 chr1 140 176 | |
| 127 chr1 100 130 | |
| 128 chr1 120 147 | |
| 129 | |
| 130 | |
| 131 Output (BedGraph format)- | |
| 132 Sorted, non-overlapping intervals, with coverage value on the 4th column:: | |
| 133 | |
| 134 chr1 100 120 1 | |
| 135 chr1 120 130 2 | |
| 136 chr1 130 140 1 | |
| 137 chr1 140 147 2 | |
| 138 chr1 147 176 1 | |
| 139 | |
| 140 ----- | |
| 141 | |
| 142 **Example 2 - with ZERO-Regions selected (assuming hg19)** | |
| 143 | |
| 144 Input (BED format)- | |
| 145 Overlapping, un-sorted intervals:: | |
| 146 | |
| 147 chr1 140 176 | |
| 148 chr1 100 130 | |
| 149 chr1 120 147 | |
| 150 | |
| 151 | |
| 152 BedGraph output will contain five columns: | |
| 153 | |
| 154 * 1. Chromosome name (or 'genome' for whole-genome coverage) | |
| 155 * 2. Coverage depth | |
| 156 * 3. The number of bases on chromosome (or genome) with depth equal to column 2. | |
| 157 * 4. The size of chromosome (or entire genome) in base pairs | |
| 158 * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2. | |
| 159 | |
| 160 **Example Output**: | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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161 |
| 1 | 162 chr2L 0 1379895 23011544 0.0599653 |
| 163 chr2L 1 837250 23011544 0.0363839 | |
| 164 chr2L 2 904442 23011544 0.0393038 | |
| 165 chr2L 3 913723 23011544 0.0397072 | |
| 166 chr2L 4 952166 23011544 0.0413778 | |
| 167 chr2L 5 967763 23011544 0.0420555 | |
| 168 chr2L 6 986331 23011544 0.0428624 | |
| 169 chr2L 7 998244 23011544 0.0433801 | |
| 170 chr2L 8 995791 23011544 0.0432735 | |
| 171 chr2L 9 996398 23011544 0.0432999 | |
| 172 | |
| 173 | |
| 174 @REFERENCES@ | |
| 175 ]]> | |
| 176 </help> | |
| 177 <expand macro="citations" /> | |
| 178 </tool> |