[2] | 1 | <tool id="gops_join_1" name="Join"> |
---|
| 2 | <description>the intervals of two queries side-by-side</description> |
---|
| 3 | <command interpreter="python">gops_join.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} -m $min -f $fill</command> |
---|
| 4 | <inputs> |
---|
| 5 | <param format="interval" name="input1" type="data" help="First query"> |
---|
| 6 | <label>Join</label> |
---|
| 7 | </param> |
---|
| 8 | <param format="interval" name="input2" type="data" help="Second query"> |
---|
| 9 | <label>with</label> |
---|
| 10 | </param> |
---|
| 11 | <param name="min" size="4" type="integer" value="1" help="(bp)"> |
---|
| 12 | <label>with min overlap</label> |
---|
| 13 | </param> |
---|
| 14 | <param name="fill" type="select" label="Return"> |
---|
| 15 | <option value="none">Only records that are joined (INNER JOIN)</option> |
---|
| 16 | <option value="right">All records of first query (fill null with ".")</option> |
---|
| 17 | <option value="left">All records of second query (fill null with ".")</option> |
---|
| 18 | <option value="both">All records of both queries (fill nulls with ".")</option> |
---|
| 19 | </param> |
---|
| 20 | </inputs> |
---|
| 21 | <outputs> |
---|
| 22 | <data format="interval" name="output" metadata_source="input1" /> |
---|
| 23 | </outputs> |
---|
| 24 | <code file="operation_filter.py"/> |
---|
| 25 | <tests> |
---|
| 26 | <test> |
---|
| 27 | <param name="input1" value="1.bed" /> |
---|
| 28 | <param name="input2" value="2.bed" /> |
---|
| 29 | <param name="min" value="1" /> |
---|
| 30 | <param name="fill" value="none" /> |
---|
| 31 | <output name="output" file="gops-join-none.dat" /> |
---|
| 32 | </test> |
---|
| 33 | <test> |
---|
| 34 | <param name="input1" value="1.bed" /> |
---|
| 35 | <param name="input2" value="2.bed" /> |
---|
| 36 | <param name="min" value="1" /> |
---|
| 37 | <param name="fill" value="right" /> |
---|
| 38 | <output name="output" file="gops-join-right.dat" /> |
---|
| 39 | </test> |
---|
| 40 | <test> |
---|
| 41 | <param name="input1" value="1.bed" /> |
---|
| 42 | <param name="input2" value="2.bed" /> |
---|
| 43 | <param name="min" value="1" /> |
---|
| 44 | <param name="fill" value="left" /> |
---|
| 45 | <output name="output" file="gops-join-left.dat" /> |
---|
| 46 | </test> |
---|
| 47 | <test> |
---|
| 48 | <param name="input1" value="1.bed" /> |
---|
| 49 | <param name="input2" value="2.bed" /> |
---|
| 50 | <param name="min" value="1" /> |
---|
| 51 | <param name="fill" value="both" /> |
---|
| 52 | <output name="output" file="gops-join-both.dat" /> |
---|
| 53 | </test> |
---|
| 54 | <test> |
---|
| 55 | <param name="input1" value="1.bed" /> |
---|
| 56 | <param name="input2" value="2.bed" /> |
---|
| 57 | <param name="min" value="500" /> |
---|
| 58 | <param name="fill" value="none" /> |
---|
| 59 | <output name="output" file="gops-join-none-500.dat" /> |
---|
| 60 | </test> |
---|
| 61 | <test> |
---|
| 62 | <param name="input1" value="1.bed" /> |
---|
| 63 | <param name="input2" value="2.bed" /> |
---|
| 64 | <param name="min" value="100" /> |
---|
| 65 | <param name="fill" value="both" /> |
---|
| 66 | <output name="output" file="gops-join-both-100.dat" /> |
---|
| 67 | </test> |
---|
| 68 | </tests> |
---|
| 69 | <help> |
---|
| 70 | |
---|
| 71 | .. class:: infomark |
---|
| 72 | |
---|
| 73 | **TIP:** If your query does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. |
---|
| 74 | |
---|
| 75 | ----- |
---|
| 76 | |
---|
| 77 | **Screencasts!** |
---|
| 78 | |
---|
| 79 | See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). |
---|
| 80 | |
---|
| 81 | .. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc |
---|
| 82 | |
---|
| 83 | ----- |
---|
| 84 | |
---|
| 85 | **Syntax** |
---|
| 86 | |
---|
| 87 | - **Where overlap** specifies the minimum overlap between intervals that allows them to be joined. |
---|
| 88 | - **Return only records that are joined** returns only the records of the first query that join to a record in the second query. This is analogous to an INNER JOIN. |
---|
| 89 | - **Return all records of first query (fill null with ".")** returns all intervals of the first query, and any intervals that do not join an interval from the second query are filled in with a period(.). This is analogous to a LEFT JOIN. |
---|
| 90 | - **Return all records of second query (fill null with ".")** returns all intervals of the second query, and any intervals that do not join an interval from the first query are filled in with a period(.). **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.** |
---|
| 91 | - **Return all records of both queries (fill nulls with ".")** returns all records from both queries, and fills on either the right or left with periods. **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.** |
---|
| 92 | |
---|
| 93 | ----- |
---|
| 94 | |
---|
| 95 | **Example** |
---|
| 96 | |
---|
| 97 | If **First query** is:: |
---|
| 98 | |
---|
| 99 | chr1 10 100 Query1.1 |
---|
| 100 | chr1 500 1000 Query1.2 |
---|
| 101 | chr1 1100 1250 Query1.3 |
---|
| 102 | |
---|
| 103 | and **Second query** is:: |
---|
| 104 | |
---|
| 105 | chr1 20 80 Query2.1 |
---|
| 106 | chr1 2000 2204 Query2.2 |
---|
| 107 | chr1 2500 3000 Query2.3 |
---|
| 108 | |
---|
| 109 | |
---|
| 110 | The four return options will generate: |
---|
| 111 | |
---|
| 112 | |
---|
| 113 | - **Return only records that are joined**:: |
---|
| 114 | |
---|
| 115 | chr1 10 100 Query1.1 chr1 20 80 Query2.1 |
---|
| 116 | |
---|
| 117 | - **Return all records of first query**:: |
---|
| 118 | |
---|
| 119 | chr1 10 100 Query1.1 chr1 20 80 Query2.1 |
---|
| 120 | chr1 500 1000 Query1.2 . . . . |
---|
| 121 | chr1 1100 1250 Query1.3 . . . . |
---|
| 122 | |
---|
| 123 | - **Return all records of second query**:: |
---|
| 124 | |
---|
| 125 | chr1 10 100 Query1.1 chr1 20 80 Query2.1 |
---|
| 126 | . . . . chr1 2000 2204 Query2.2 |
---|
| 127 | . . . . chr1 2500 3000 Query2.3 |
---|
| 128 | |
---|
| 129 | - **Return all records of both queries**:: |
---|
| 130 | |
---|
| 131 | chr1 10 100 Query1.1 chr1 20 80 Query2.1 |
---|
| 132 | chr1 500 1000 Query1.2 . . . . |
---|
| 133 | chr1 1100 1250 Query1.3 . . . . |
---|
| 134 | . . . . chr1 2000 2204 Query2.2 |
---|
| 135 | . . . . chr1 2500 3000 Query2.3 |
---|
| 136 | |
---|
| 137 | |
---|
| 138 | </help> |
---|
| 139 | </tool> |
---|