new screenshoot added

command/docs/use_cases.rst

@@ -25,7 +25,7 @@ We start by selecting Experiments from Data collection (top left corner) then we
 Parse Experiment, Platform and Samples
 ++++++++++++++++++++++++++++++++++++++
 
-Since we have a new platform (`GPL90 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL90>`_) never imported before into COMMAND>_ for this compendium, we retrieve the :download:`gene sequences <YG_S98.probe_tab>` for this platform from the `Affymetrix Support sitewebsite <http://www.affymetrix.com/support/technical/byproduct.affx?product=yeast>`_. 
+Since we have a new platform (`GPL90 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL90>`_) never imported before into COMMAND>_ for this compendium,  we retrieve the sequences associated to the Affymetrix probe ids ( :download:`YG_S98 probes <YG_S98.probe_tab>` ) for this platform from the `Affymetrix Support sitewebsite <http://www.affymetrix.com/support/technical/byproduct.affx?product=yeast>`_. 
 
 From Experiments (Data collection Menu) we highlight the selected experiment (GSE8536 here) and click the Parse/Import experiment from the bottom bar.
 On the main window you can see that the Experiment tab is populated with metadata gathered from the publicDB (GEO here).
@@ -41,33 +41,50 @@ Now we can start parsing the Experiment, the Platform(s) and the Samples.
 
 Being a dataset retrieved from GEO we take advantage of the .soft file downloaded (see GEO Documentation for a description of this type of file):
 
-Select GSE8536_family.soft and click the 'Use assignment script to assign files to experiment entities' icon on the bottom-right. A dialog will show-up:
+Select `GSE8536_family.soft` and click the `Use assignment script to assign files to experiment entities` icon on the bottom-right. A dialog will show-up:
+
 - Script > assign_all.py > Only selected files
 - Experiment tab > Script: > soft_experiment.py, Execution order: 1
 - Platform tab > Script: > soft_platform.py, Execution order: 1
 - Sample tab > Script: > soft_sample.py, Execution order: 1
 - Run assignment script
 
-In order to map properly the probes to genes we need to retrieve the sequences associated to the Affymetrix probe ids for Yeast. We’ll use this file downloaded from the `Affymetrix Support site <http://www.affymetrix.com/support/technical/byproduct.affx?product=yeast>`_. We import the annotation in the File assignment section of Experiment files clicking the upload icon on the bottom of the page. 
+.. _Case01_03b:
+.. figure::  _static/Case01_03b.png
+   :align:   center
+
+Now in order to parse the new platform we are going to use the sequences associated to the Affymetrix probe ids we have already downloaded. We import the annotation ( :download:`YG_S98 probes <YG_S98.probe_tab>` ) in the `File assignment` section of `Experiment files` clicking the upload icon on the bottom of the page. 
 
 Now we associate the file to the platform:
-- In Experiment files Section > File Assignment > Select the uploaded  file and on the Assign files dialog:
-- Script: match_entity_type_param.py
-- Param: platform
+
+- In Experiment files Section > File Assignment select the uploaded file (YG_S98.probe_tab) and click `Use assignment script to assign files to experiment entities`. On the Assign files dialog:
+
+- Script: assign_all.py
+- Param: 
 - Only selected files checked  (default)
-- Platform tab > Script: > gpr_platform.py ;  Parameters: 0,Probe X|Probe Y,Probe Sequence ; Execution order: 2
+- Platform tab > Script: `gpr_platform.py` , Parameters: 0,Probe X|Probe Y,Probe Sequence , Execution order: 2
 - Run assignment script
 
-Note: the Parameters assigned to the gpr_platform.py script specify to not skip any line, use the combination of Probe X and Probe Y columns to create an unique id for the cel files and indicate the sequences for the probes are in the Probe Sequence column.
+.. _Case01_03c:
+.. figure::  _static/Case01_03c.png
+   :align:   center
 
 .. Note::
-   Thi is a once time procedure: from now on we can use this platform for all related experiments.
+
+  - the Parameters assigned to the `gpr_platform.py` script specify to not skip any line, use the combination of Probe X and Probe Y columns to create an unique id for the cel files and indicate the sequences for the probes are in the Probe Sequence column.
+  - The parsing of the Platform is a once time procedure: from now on we can use this platform for all related experiments.
 
 Now we parse the Affymetrix cel files (sample files):
-- In Experiment Files Section  we use as filter CEL and select all files >  click the 'Use assignment script to assign files to experiment entities' icon on the bottom-right corner and the Assign files and scripts to experiment structure dialog will pop-up:
-- Script > match_sample_name.py > Only selected files
-- Sample > Script: > cell_sample.py, Execution order: 2
-- > Run assignment script
+
+- In Experiment files Section > File Assignment  we use CEL as filter and select all files > click the `Use assignment script to assign files to experiment entities` icon on the bottom-right corner and the Assign files and scripts to experiment structure dialog will pop-up:
+- Script > match_entity_name.py 
+- Only selected files (default) checked
+- Sample tab > Script: `cell_sample.py`, Execution order: 2
+- Run assignment script
+
+.. _Case01_03d:
+.. figure::  _static/Case01_03d.png
+   :align:   center
 
 Finally, in the Sample tab of the main interface click Run Selected (bottom-right corner). After a while  your samples will be parsed.