--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/new_operations/join.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,139 @@
+<tool id="gops_join_1" name="Join">
+  <description>the intervals of two datasets side-by-side</description>
+  <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>
+  <inputs>
+    <param format="interval" name="input1" type="data" help="First dataset">
+      <label>Join</label>
+    </param>
+    <param format="interval" name="input2" type="data" help="Second dataset">
+      <label>with</label>
+    </param>
+    <param name="min" size="4" type="integer" value="1" help="(bp)">
+      <label>with min overlap</label>
+    </param>
+  <param name="fill" type="select" label="Return">
+    <option value="none">Only records that are joined (INNER JOIN)</option>
+    <option value="right">All records of first dataset (fill null with ".")</option>
+    <option value="left">All records of second dataset (fill null with ".")</option>
+    <option value="both">All records of both datasets (fill nulls with ".")</option>
+  </param>
+   </inputs>
+  <outputs>
+    <data format="interval" name="output" metadata_source="input1" />
+  </outputs>
+  <code file="operation_filter.py"/>
+  <tests>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2.bed" />
+      <param name="min" value="1" />
+      <param name="fill" value="none" />
+      <output name="output" file="gops-join-none.dat" />
+    </test>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2.bed" />
+      <param name="min" value="1" />
+      <param name="fill" value="right" />
+      <output name="output" file="gops-join-right.dat" />
+    </test>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2.bed" />
+      <param name="min" value="1" />
+      <param name="fill" value="left" />
+      <output name="output" file="gops-join-left.dat" />
+    </test>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2.bed" />
+      <param name="min" value="1" />
+      <param name="fill" value="both" />
+      <output name="output" file="gops-join-both.dat" />
+    </test>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2.bed" />
+      <param name="min" value="500" />
+      <param name="fill" value="none" />
+      <output name="output" file="gops-join-none-500.dat" />
+    </test>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2.bed" />
+      <param name="min" value="100" />
+      <param name="fill" value="both" />
+      <output name="output" file="gops-join-both-100.dat" />
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**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.
+
+-----
+
+**Screencasts!**
+
+See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
+
+.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
+
+-----
+
+**Syntax**
+
+- **Where overlap** specifies the minimum overlap between intervals that allows them to be joined.
+- **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.
+- **Return all records of first dataset (fill null with &quot;.&quot;)** 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.
+- **Return all records of second dataset (fill null with &quot;.&quot;)** 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.**
+- **Return all records of both datasets (fill nulls with &quot;.&quot;)** 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.**
+
+-----
+
+**Example**
+
+If **First dataset** is::
+
+   chr1 10   100  Query1.1
+   chr1 500  1000 Query1.2
+   chr1 1100 1250 Query1.3
+
+and **Second dataset** is::
+
+   chr1 20   80   Query2.1
+   chr1 2000 2204 Query2.2
+   chr1 2500 3000 Query2.3
+
+
+The four return options will generate:
+
+
+- **Return only records that are joined**::
+
+   chr1 10 100 Query1.1 chr1 20 80 Query2.1
+
+- **Return all records of first dataset**::
+
+   chr1 10   100  Query1.1 chr1 20 80 Query2.1
+   chr1 500  1000 Query1.2 .    .  .  .
+   chr1 1100 1250 Query1.3 .    .  .  .
+
+- **Return all records of second dataset**::
+
+   chr1 10 100 Query1.1 chr1 20   80   Query2.1
+   .    .  .   .        chr1 2000 2204 Query2.2
+   .    .  .   .        chr1 2500 3000 Query2.3
+
+- **Return all records of both datasets**::
+
+   chr1 10   100  Query1.1 chr1 20   80   Query2.1
+   chr1 500  1000 Query1.2 .    .    .    .
+   chr1 1100 1250 Query1.3 .    .    .    .
+   .    .    .    .        chr1 2000 2204 Query2.2
+   .    .    .    .        chr1 2500 3000 Query2.3
+   
+
+</help>
+</tool>
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