Mercurial > repos > iuc > bedtools
annotate macros.xml @ 26:c0fbce5dc84a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
| author | iuc |
|---|---|
| date | Mon, 17 Oct 2016 10:13:20 -0400 |
| parents | a2d4c30ba2f9 |
| children | f0aca67fdb71 |
| rev | line source |
|---|---|
| 8 | 1 <macros> |
| 2 <xml name="requirements"> | |
| 3 <requirements> | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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changeset
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4 <requirement type="package" version="2.26.0gx">bedtools</requirement> |
| 8 | 5 <yield/> |
| 6 </requirements> | |
| 7 </xml> | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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changeset
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8 <token name="@WRAPPER_VERSION@">2.26.0</token> |
| 8 | 9 <xml name="stdio"> |
| 10 <stdio> | |
| 11 <!-- Anything other than zero is an error --> | |
| 12 <exit_code range="1:" /> | |
| 13 <exit_code range=":-1" /> | |
| 14 <!-- In case the return code has not been set propery check stderr too --> | |
| 15 <regex match="Error:" /> | |
| 16 <regex match="Exception:" /> | |
| 17 </stdio> | |
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542d2008a462
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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18 <version_command>bedtools --version</version_command> |
| 8 | 19 </xml> |
| 20 <xml name="reciprocal"> | |
| 21 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" | |
| 22 label="Require that the fraction of overlap be reciprocal for A and B" | |
| 23 help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B. (-r)" /> | |
| 24 </xml> | |
| 25 <xml name="overlap"> | |
| 26 <param name="overlap" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" help="Default is 1E-9, i.e. 1bp. (-f)"/> | |
| 27 </xml> | |
| 28 <xml name="strand2"> | |
| 29 <param name="strand" type="select" label="Calculation based on strandedness?"> | |
| 30 <option value="" selected="True">Overlaps on either strand</option> | |
| 31 <option value="-s">Only overlaps occurring on the **same** strand.</option> | |
| 32 <option value="-S">Only overlaps occurring on the **opposite** strand.</option> | |
| 33 </param> | |
| 34 </xml> | |
| 35 <xml name="seed"> | |
| 36 <conditional name="seed"> | |
| 37 <param name="seed_choose" type="select" label="Choose Seed?" help="(-seed)"> | |
| 38 <option value="False" selected="True">Random Shuffling</option> | |
| 39 <option value="True">Choose fixed seed</option> | |
| 40 </param> | |
| 41 <when value="True"> | |
| 42 <param name="seed" type="integer" value="12345" label="Enter Seed" /> | |
| 43 </when> | |
| 44 <when value="False" /> | |
| 45 </conditional> | |
| 46 </xml> | |
| 47 <xml name="split"> | |
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542d2008a462
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
8
diff
changeset
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48 <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" |
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542d2008a462
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
8
diff
changeset
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49 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." |
| 8 | 50 help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data. (-split)" /> |
| 51 </xml> | |
| 52 <xml name="genome"> | |
| 53 <param format="tabular" name="genome" type="data" label="Genome file" /> | |
| 54 <!--TODO: make use of: ${chromInfo} --> | |
| 55 </xml> | |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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changeset
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56 <xml name="closest_D_option"> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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changeset
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57 <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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58 label="Ignore features in B that are upstream of features in A" |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
16
diff
changeset
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59 help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" /> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
16
diff
changeset
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60 |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
16
diff
changeset
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61 <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue="" |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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62 label="Ignore features in B that are downstream of features in A" |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
16
diff
changeset
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63 help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" /> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
16
diff
changeset
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64 |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
16
diff
changeset
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65 <param name="fu" type="boolean" checked="false" truevalue="-fu" falsevalue="" |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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66 label="Choose first from features in B that are upstream of features in A" |
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17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
16
diff
changeset
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67 help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-fu)" /> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
16
diff
changeset
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68 |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
16
diff
changeset
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69 <param name="fd" type="boolean" checked="false" truevalue="-fd" falsevalue="" |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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70 label="Choose first from features in B that are downstream of features in A" |
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17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
16
diff
changeset
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71 help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-fd)" /> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
16
diff
changeset
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72 </xml> |
| 8 | 73 <xml name="addition"> |
| 74 <conditional name="addition"> | |
| 75 <param name="addition_select" type="select" label="Choose what you want to do"> | |
| 76 <option value="b" selected="True">Increase the BED/GFF/VCF entry by the same number base pairs in each direction.</option> | |
| 77 <option value="lr">Increase by Start Coordinate and End Coordinate</option> | |
| 78 </param> | |
| 79 <when value="b"> | |
| 80 <param name="b" value="1" label="Number of base pairs" type="integer" /> | |
| 81 </when> | |
| 82 <when value="lr"> | |
| 83 <param name="l" type="integer" value="0" label="The number of base pairs to subtract from the start coordinate" /> | |
| 84 <param name="r" type="integer" value="0" label="The number of base pairs to add to the end coordinate" /> | |
| 85 </when> | |
| 86 </conditional> | |
| 87 </xml> | |
| 88 <xml name="print_header"> | |
| 89 <param name="header" type="boolean" checked="False" truevalue="-header" falsevalue="" | |
| 90 label="Print the header from the A file prior to results" help="(-header)" /> | |
| 91 </xml> | |
| 92 <!-- TODO this is currently not used, but we should make use of it --> | |
| 93 <xml name="genome_validator"> | |
| 94 <validator type="unspecified_build" /> | |
| 95 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> | |
| 96 </xml> | |
| 97 | |
| 98 <!-- ToDo column_picker --> | |
| 99 <xml name="choose_columns"> | |
| 100 <param name="cols" type="text" value="" | |
| 101 label="Specify the column(s) that should be summarized" | |
| 102 help="comma separated (-c)"> | |
| 103 <sanitizer invalid_char=""> | |
| 104 <valid initial="string.digits"><add value=","/></valid> | |
| 105 </sanitizer> | |
| 106 </param> | |
| 107 </xml> | |
| 108 | |
| 109 <token name="@C_AND_O_ARGUMENT@"> | |
| 110 #set $col = list() | |
| 111 #set $op = list() | |
| 112 #for $item in $c_and_o_argument_repeat: | |
| 113 #silent $col.append( str($item.col) ) | |
| 114 #silent $op.append( str($item.operation) ) | |
| 115 #end for | |
| 116 #if $col: | |
| 117 -c #echo ','.join($col)# | |
| 118 -o #echo ','.join($op)# | |
| 119 #end if | |
| 120 </token> | |
| 121 | |
| 122 <xml name="c_and_o_argument"> | |
| 123 <repeat name="c_and_o_argument_repeat" title="Applying operations to columns from merged intervals" min="0"> | |
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e30113df8cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 7b8a4ffc823f4dab194f1c629b7e83277dbe4337
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124 <yield /> |
| 8 | 125 <expand macro="choose_operations"> |
| 126 <expand macro="math_options" /> | |
| 127 <expand macro="additional_math_options" /> | |
| 128 </expand> | |
| 129 </repeat> | |
| 130 </xml> | |
| 131 | |
| 132 | |
| 133 <xml name="choose_operations"> | |
| 134 <param name="operation" type="select" label="Specify the operation"> | |
| 135 <yield /> | |
| 136 </param> | |
| 137 </xml> | |
| 138 | |
| 139 <xml name="math_options"> | |
| 140 <option value="sum" selected="True">Sum - numeric only</option> | |
| 141 <option value="min">Min - numeric only</option> | |
| 142 <option value="max">Max - numeric only</option> | |
| 143 <option value="absmin">AbsMin - numeric only</option> | |
| 144 <option value="absmax">AbsMax - numeric only</option> | |
| 145 <option value="mean">Mean - numeric only</option> | |
| 146 <option value="median">Median - numeric only</option> | |
| 147 <option value="mode">Mode - numeric only</option> | |
| 148 <option value="antimode">Antimode - numeric only</option> | |
| 149 <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option> | |
| 150 </xml> | |
| 151 <xml name="additional_math_options"> | |
| 152 <option value="count">Count - numeric or text</option> | |
| 153 <option value="count_disctinct">Count Distinct - numeric or text</option> | |
| 154 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option> | |
| 155 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option> | |
| 156 </xml> | |
| 157 <token name="@REFERENCES@"> | |
| 158 <![CDATA[ | |
| 159 ------ | |
| 160 | |
| 161 This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_. | |
| 162 | |
| 163 .. _bedtools package: https://github.com/arq5x/bedtools2 | |
| 164 .. _Quinlan laboratory: http://cphg.virginia.edu/quinlan/ | |
| 165 | |
| 166 | |
| 167 **Citation** | |
| 168 | |
| 169 If you use this tool in Galaxy, please cite: | |
| 170 | |
| 171 Bjoern A. Gruening (2014), `Galaxy wrapper <https://github.com/bgruening/galaxytools>`_ | |
| 172 ]]> | |
| 173 </token> | |
| 174 <xml name="citations"> | |
| 175 <citations> | |
| 176 <citation type="doi">10.1093/bioinformatics/btq033</citation> | |
| 177 <yield /> | |
| 178 </citations> | |
| 179 </xml> | |
| 180 </macros> |