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1 <tool id="gops_join_1" name="Join">
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2 <description>the intervals of two datasets side-by-side</description>
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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>
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4 <inputs>
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5 <param format="interval" name="input1" type="data" help="First dataset">
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6 <label>Join</label>
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7 </param>
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8 <param format="interval" name="input2" type="data" help="Second dataset">
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9 <label>with</label>
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10 </param>
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11 <param name="min" size="4" type="integer" value="1" help="(bp)">
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12 <label>with min overlap</label>
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13 </param>
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14 <param name="fill" type="select" label="Return">
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15 <option value="none">Only records that are joined (INNER JOIN)</option>
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16 <option value="right">All records of first dataset (fill null with ".")</option>
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17 <option value="left">All records of second dataset (fill null with ".")</option>
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18 <option value="both">All records of both datasets (fill nulls with ".")</option>
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19 </param>
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20 </inputs>
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21 <outputs>
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22 <data format="interval" name="output" metadata_source="input1" />
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23 </outputs>
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24 <code file="operation_filter.py"/>
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25 <tests>
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26 <test>
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27 <param name="input1" value="1.bed" />
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28 <param name="input2" value="2.bed" />
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29 <param name="min" value="1" />
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30 <param name="fill" value="none" />
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31 <output name="output" file="gops-join-none.dat" />
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32 </test>
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33 <test>
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34 <param name="input1" value="1.bed" />
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35 <param name="input2" value="2.bed" />
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36 <param name="min" value="1" />
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37 <param name="fill" value="right" />
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38 <output name="output" file="gops-join-right.dat" />
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39 </test>
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40 <test>
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41 <param name="input1" value="1.bed" />
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42 <param name="input2" value="2.bed" />
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43 <param name="min" value="1" />
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44 <param name="fill" value="left" />
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45 <output name="output" file="gops-join-left.dat" />
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46 </test>
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47 <test>
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48 <param name="input1" value="1.bed" />
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49 <param name="input2" value="2.bed" />
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50 <param name="min" value="1" />
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51 <param name="fill" value="both" />
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52 <output name="output" file="gops-join-both.dat" />
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53 </test>
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54 <test>
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55 <param name="input1" value="1.bed" />
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56 <param name="input2" value="2.bed" />
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57 <param name="min" value="500" />
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58 <param name="fill" value="none" />
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59 <output name="output" file="gops-join-none-500.dat" />
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60 </test>
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61 <test>
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62 <param name="input1" value="1.bed" />
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63 <param name="input2" value="2.bed" />
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64 <param name="min" value="100" />
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65 <param name="fill" value="both" />
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66 <output name="output" file="gops-join-both-100.dat" />
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67 </test>
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68 </tests>
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69 <help>
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70
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71 .. class:: infomark
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72
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73 **TIP:** If your dataset 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.
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74
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75 -----
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76
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77 **Screencasts!**
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78
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79 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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80
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81 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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82
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83 -----
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84
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85 **Syntax**
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86
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87 - **Where overlap** specifies the minimum overlap between intervals that allows them to be joined.
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88 - **Return only records that are joined** returns only the records of the first dataset that join to a record in the second dataset. This is analogous to an INNER JOIN.
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89 - **Return all records of first dataset (fill null with ".")** returns all intervals of the first dataset, and any intervals that do not join an interval from the second dataset are filled in with a period(.). This is analogous to a LEFT JOIN.
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90 - **Return all records of second dataset (fill null with ".")** returns all intervals of the second dataset, and any intervals that do not join an interval from the first dataset 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.**
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91 - **Return all records of both datasets (fill nulls with ".")** returns all records from both datasets, 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.**
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92
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93 -----
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94
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95 **Example**
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96
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97 If **First dataset** is::
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98
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99 chr1 10 100 Query1.1
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100 chr1 500 1000 Query1.2
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101 chr1 1100 1250 Query1.3
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102
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103 and **Second dataset** is::
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104
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105 chr1 20 80 Query2.1
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106 chr1 2000 2204 Query2.2
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107 chr1 2500 3000 Query2.3
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108
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109
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110 The four return options will generate:
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111
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112
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113 - **Return only records that are joined**::
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114
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115 chr1 10 100 Query1.1 chr1 20 80 Query2.1
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116
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117 - **Return all records of first dataset**::
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118
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119 chr1 10 100 Query1.1 chr1 20 80 Query2.1
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120 chr1 500 1000 Query1.2 . . . .
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121 chr1 1100 1250 Query1.3 . . . .
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122
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123 - **Return all records of second dataset**::
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124
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125 chr1 10 100 Query1.1 chr1 20 80 Query2.1
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126 . . . . chr1 2000 2204 Query2.2
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127 . . . . chr1 2500 3000 Query2.3
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128
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129 - **Return all records of both datasets**::
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130
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131 chr1 10 100 Query1.1 chr1 20 80 Query2.1
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132 chr1 500 1000 Query1.2 . . . .
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133 chr1 1100 1250 Query1.3 . . . .
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134 . . . . chr1 2000 2204 Query2.2
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135 . . . . chr1 2500 3000 Query2.3
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136
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137
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138 </help>
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139 </tool> |
