consolidate protocols -> 1 general consolidate

protocols/96_well_plate_filling/README.md

@@ -9,7 +9,6 @@
 * Basic Pipetting
 	* Plate Filling
 
-
 ## Description
 This protocol has been merged into [Copy source plate to N plates with 8-channel](./plate_copying)
 

protocols/consolidate/README.md

@@ -0,0 +1,43 @@
+# Consolidate multiple wells into one
+
+### Author
+[Opentrons](https://opentrons.com/)
+
+### Partner
+[Phdbiotech Inc.](http://www.phdbiotech.com/)
+
+## Categories
+* Basic Pipetting
+	* Plate Consolidation
+
+## Description
+With this protocol, your robot can consolidate the contents of an entire 96 well plate into a single 1.5 mL microcentrifuge tube using a p200 single channel pipette, without tip changes. Use this protocol when combining DNA libraries and/or PCR products from an entire plate. This protocol is best suited for consolidations where sterility is not a concern.
+
+### Time Estimate
+
+### Robot
+* [OT PRO](https://opentrons.com/ot-one-pro)
+* [OT Standard](https://opentrons.com/ot-one-standard)  
+* [OT Hood](https://opentrons.com/ot-one-hood)
+
+### Modules
+
+
+### Reagents
+
+
+## Process
+1. Input your desired volume into the "consolidate volume" field above. This is the volume that will be pulled from each well of the plate, *not* the total final volume that will go into the tube.
+2. Download your protocol.
+3. Upload your protocol into the [OT App](http://opentrons.com/ot-app).
+4. Set up your deck according to the deck map below.
+5. Calibrate your tiprack, pipette, and labware using the OT app. For calibration tips, check out our [support articles](https://support.opentrons.com/getting-started/software-setup/calibrating-the-pipettes).
+6. Hit "run".
+7. The robot will pick up one tip and aspirate your defined volume from each well of the 96 well plate, transferring that volume from each well into your microcentrifuge tube.
+
+### Additional Notes
+* One tip is used throughout the entire run. If you want to implement tip changes, modify your pipette size, or change your labware, see our [API documentation](https://docs.opentrons.com) for tips on how to modify your Python script.
+
+
+
+###### Internal

protocols/consolidate/consolidate.py

@@ -0,0 +1,59 @@
+from opentrons import containers, instruments
+from otcustomizers import StringSelection
+
+trash = containers.load('trash-box', 'B2')
+
+
+def tiprack_from_pipette(pipette_vol):
+    if pipette_vol <= 10:
+        return 'tiprack-10ul'
+    if 1000 > pipette_vol > 10:
+        return 'tiprack-200ul'
+    if pipette_vol == 1000:
+        return 'tiprack-1000ul'
+    raise ValueError('No known tiprack for a p{} pipette'.format(pipette_vol))
+
+
+def run_custom_protocol(
+        pipette_axis: StringSelection(
+            'B (left side)', 'A (right side)')='B (left side)',
+        pipette_model: StringSelection(
+            'p200', 'p100', 'p50', 'p20', 'p10', 'p1000')='p200',
+        consolidate_volume: float=20.0,
+        source_container: StringSelection(
+            '96-flat', 'tube-rack-2ml')='96-flat',
+        number_of_source_wells: int=4,
+        destination_container: StringSelection(
+            '96-flat', 'tube-rack-2ml')='96-flat',
+        destination_well: str='A1',
+        tip_reuse_strategy: StringSelection(
+            'reuse one tip', 'new tip each time')='reuse one tip'):
+
+    pipette_max_vol = int(pipette_model[1:])
+    new_tip = 'always' if tip_reuse_strategy == 'new tip each time' else 'once'
+    tip_rack = containers.load(tiprack_from_pipette(pipette_max_vol), 'A1')
+
+    source = containers.load(source_container, 'D1')
+    dest = containers.load(destination_container, 'B1')
+
+    try:
+        dest_well = dest.wells(destination_well)
+    except ValueError:
+        raise RuntimeError(
+            'Invalid destination well "{}". Expected well name like A1, H11, '
+            .format(destination_well) + 'etc. The destination plate may not ' +
+            'have a well of that name (eg a 96-well plate has no well "T18")')
+
+    pipette = instruments.Pipette(
+        axis='b',
+        max_volume=pipette_max_vol,
+        min_volume=pipette_max_vol / 10,
+        tip_racks=[tip_rack],
+        trash_container=trash
+    )
+
+    pipette.consolidate(
+        consolidate_volume,
+        source[:number_of_source_wells],
+        dest_well,
+        new_tip=new_tip)

protocols/consolidate_plate_to_tube/README.md

@@ -1,43 +1,27 @@
-# Consolidate 96 Well Plate to Microcentrifuge Tube
+# REDIRECT: Consolidate 96 Well Plate to Microcentrifuge Tube
 
 ### Author
 [Opentrons](https://opentrons.com/)
 
 ### Partner
-[Phdbiotech Inc.](http://www.phdbiotech.com/)
 
 ## Categories
 * Basic Pipetting
 	* Plate Consolidation
 
 ## Description
-With this protocol, your robot can consolidate the contents of an entire 96 well plate into a single 1.5 mL microcentrifuge tube using a p200 single channel pipette, without tip changes. Use this protocol when combining DNA libraries and/or PCR products from an entire plate. This protocol is best suited for consolidations where sterility is not a concern.
+This protocol has been merged into [Consolidate](./consolidate)
 
 ### Time Estimate
 
 ### Robot
-* [OT PRO](https://opentrons.com/ot-one-pro)
-* [OT Standard](https://opentrons.com/ot-one-standard)  
-* [OT Hood](https://opentrons.com/ot-one-hood) 
 
 ### Modules
 
-
 ### Reagents
 
-
 ## Process
-1. Input your desired volume into the "consolidate volume" field above. This is the volume that will be pulled from each well of the plate, *not* the total final volume that will go into the tube.
-2. Download your protocol.
-3. Upload your protocol into the [OT App](http://opentrons.com/ot-app).
-4. Set up your deck according to the deck map below.
-5. Calibrate your tiprack, pipette, and labware using the OT app. For calibration tips, check out our [support articles](https://support.opentrons.com/getting-started/software-setup/calibrating-the-pipettes).
-6. Hit "run".
-7. The robot will pick up one tip and aspirate your defined volume from each well of the 96 well plate, transferring that volume from each well into your microcentrifuge tube.
 
 ### Additional Notes
-* One tip is used throughout the entire run. If you want to implement tip changes, modify your pipette size, or change your labware, see our [API documentation](https://docs.opentrons.com) for tips on how to modify your Python script.
-
-
 
 ###### Internal