Recent changes to Galaxy Options

WikiPage Galaxy Options modified by Jesse Erdmann

Jesse Erdmann — Fri, 02 Dec 2011 16:12:38 -0000

--- v18 
+++ v19 
@@ -134,5 +134,5 @@
 
 
 One of the few cases it makes sense to not go ahead and call CIS for a project is when a new set of data is being added for future merging with another project.  If CIS calling is not needed, there are no further options to configure.
-![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_inserts_only.png)
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_choose_inserts_only.png)
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WikiPage Galaxy Options modified by Jesse Erdmann

Jesse Erdmann — Thu, 01 Dec 2011 21:36:45 -0000

--- v17 
+++ v18 
@@ -93,46 +93,46 @@
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-If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+The user has the choice of whether or not to call CIS on a project.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_desired_results.png)
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-If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+In most cases, CIS will be called.  This requires further input.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_CIS_calls.png)
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-If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+Currently metadata describing the libraries is used in two ways.  The first is to create subsets of libraries to call CIS on based on the metadata tags and the second is to aid in filtering projects later on in creating a list of projects to re-calculate or merge. 
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_metadata_options.png)
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-If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+With transposons local hopping can hopelessly clutter the area around the original site of the mutagen drowning out all signal with noise.  Currently the remedy is to omit the chromosomes hosting the donor sites.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_omit_chromosomes.png)
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-If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+A default set of features is provided, however it is unlikely to be suitable for many experiments.  The default is here in the event that the user isn't all that interested in the CIS annotation and just wants the relevant intervals.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_annotation.png)
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-If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+Annotating CIS calls requires a BED file containing the features to annotate with.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_custom_annotation.png)
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-If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+The default values for CIS calculation parameters should be reasonable, however the user does have the option to change them.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_CIS_parameters.png)
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-If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+The five CIS calling parameters start with their defaults when a user chooses to customize them.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_CIS_custom_parameters.png)
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-If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+One of the few cases it makes sense to not go ahead and call CIS for a project is when a new set of data is being added for future merging with another project.  If CIS calling is not needed, there are no further options to configure.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_inserts_only.png)
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WikiPage Galaxy Options modified by Jesse Erdmann

Jesse Erdmann — Thu, 01 Dec 2011 21:20:04 -0000

--- v16 
+++ v17 
@@ -129,7 +129,7 @@
 
 
 If a predefined config file is used, the Galaxy interface has very few inputs to enter.
-![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_uCIS_custom_parameters.png)
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_CIS_custom_parameters.png)
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WikiPage Galaxy Options modified by Jesse Erdmann

Jesse Erdmann — Thu, 01 Dec 2011 21:18:42 -0000

--- v15 
+++ v16 
@@ -18,76 +18,121 @@
                 * Matching projects using metadata
     * Predefined Configuration File
     * To call CIS or not to call CIS...
-        * Call CIS
+        * Call CIS
             * Providing metadata
-            * Omit chromosomes from calculations
-            * Annotation
-                * Custom annotation file
-            * CIS parameters
-                * Setting custom CIS calling parameters
+            * Omit chromosomes from calculations
+            * Annotation
+                * Custom annotation file
+            * CIS parameters
+                * Setting custom CIS calling parameters
         * Don't call CIS
 
 
 This is the default view of TAPDANCE in galaxy after clicking the link in the tool bar.  Each input item will be discussed below as well as any changes that may result in the view.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_default_view.png)
 top
 
 
 The first choice a user is presented with is whether they would like to define the project parameters using Galaxy or whether to upload and use a predefined config file.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_specify_or_predef.png)
 top
 
 
 There are three options for starting points in Galaxy, raw sequences, re-running a previous project or merging multiple existing projects.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_starting_point.png)
 top
 
 
 Choosing to start with sequences results in the following options.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_start_w_fastX.png)
 top
 
 
 There is a default value for the mutagen sequence, but it is a fairly narrow range of experiments it will be useful for.  TAPDANCE will attempt to match and strip the provided mutagen sequence(s) between the barcode and genomic sequence in the provided experimental sequences.  Any experimental sequences that do not match a mutagen sequence are not used in subsequent steps of the TAPDANCE process.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_mutagens.png)
 top
 
 
 Entering a custom sequence and its relavent help text.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_custom_mutagen.png)
 top
 
 
 Choose the reference genome for TAPDANCE to call Bowtie with for sequence alignment.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_reference_genome.png)
 top
 
 
 When an existing project is the chosen starting point, the following options are available.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_start_w_exist.png)
 top
 
 
 Merging existing projects is very similar to re-running an existing project.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_start_w_merge.png)
 top
 
 
 To populate the list of projects to select from, the List TAPDANCE Projects tools needs to be invoked.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/List_projects.png)
 top
 
 
 The easiest route is to simply list all available projects.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/List_project_options.png)
 top
 
 
 If the list of available projects is impractically long, using metadata tags to filter the list returned is useful.  The returned list will only contain projects where at least one of the libraries had at least one of the tags entered on the form.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/List_project_add_tag.png)
 top
 
 
 If a predefined config file is used, the Galaxy interface has very few inputs to enter.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_use_predef.png)
+top
+
+
+If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_desired_results.png)
+top
+
+
+If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_CIS_calls.png)
+top
+
+
+If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_metadata_options.png)
+top
+
+
+If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_omit_chromosomes.png)
+top
+
+
+If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_annotation.png)
+top
+
+
+If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_custom_annotation.png)
+top
+
+
+If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_CIS_parameters.png)
+top
+
+
+If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_uCIS_custom_parameters.png)
+top
+
+
+If a predefined config file is used, the Galaxy interface has very few inputs to enter.
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_inserts_only.png)
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WikiPage Galaxy Options modified by Jesse Erdmann

Jesse Erdmann — Thu, 01 Dec 2011 21:11:53 -0000

--- v14 
+++ v15 
@@ -1,4 +1,5 @@
 
+Most of the options available from the Galaxy interface to TAPDANCE are documented below.
 
 * Default View
 * Specify options in Galaxy or use a predefined config file

WikiPage Galaxy Options modified by Jesse Erdmann

Jesse Erdmann — Thu, 01 Dec 2011 21:02:11 -0000

--- v13 
+++ v14 
@@ -16,6 +16,15 @@
                 * All available projects
                 * Matching projects using metadata
     * Predefined Configuration File
+    * To call CIS or not to call CIS...
+        * Call CIS
+            * Providing metadata
+            * Omit chromosomes from calculations
+            * Annotation
+                * Custom annotation file
+            * CIS parameters
+                * Setting custom CIS calling parameters
+        * Don't call CIS
 
 
 This is the default view of TAPDANCE in galaxy after clicking the link in the tool bar.  Each input item will be discussed below as well as any changes that may result in the view.

WikiPage Galaxy Options modified by Jesse Erdmann

Jesse Erdmann — Thu, 01 Dec 2011 20:47:42 -0000

--- v12 
+++ v13 
@@ -6,44 +6,50 @@
         * FastX
             * Mutagen sequence(s) to match
                 * Custom mutagen sequences
+            * Reference Genome
         * Existing Project
             * Build a project List
                 * All available projects
                 * Matching projects using metadata
         * Merge Existing Projects
             * Build a project List
                 * All available projects
                 * Matching projects using metadata
     * Predefined Configuration File
 
 
 This is the default view of TAPDANCE in galaxy after clicking the link in the tool bar.  Each input item will be discussed below as well as any changes that may result in the view.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_default_view.png)
 top
 
 
 The first choice a user is presented with is whether they would like to define the project parameters using Galaxy or whether to upload and use a predefined config file.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_specify_or_predef.png)
 top
 
 
 There are three options for starting points in Galaxy, raw sequences, re-running a previous project or merging multiple existing projects.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_starting_point.png)
 top
 
 
 Choosing to start with sequences results in the following options.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_start_w_fastX.png)
 top
 
 
 There is a default value for the mutagen sequence, but it is a fairly narrow range of experiments it will be useful for.  TAPDANCE will attempt to match and strip the provided mutagen sequence(s) between the barcode and genomic sequence in the provided experimental sequences.  Any experimental sequences that do not match a mutagen sequence are not used in subsequent steps of the TAPDANCE process.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_mutagens.png)
 top
 
 
-Entering a custom sequence and its relavent help text
+Entering a custom sequence and its relavent help text.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_custom_mutagen.png)
+top
+
+
+Choose the reference genome for TAPDANCE to call Bowtie with for sequence alignment.
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_reference_genome.png)
 top

WikiPage Galaxy Options modified by Jesse Erdmann

Jesse Erdmann — Thu, 01 Dec 2011 20:42:50 -0000

--- v11 
+++ v12 
@@ -5,39 +5,45 @@
     * Specify options in Galaxy
         * FastX
             * Mutagen sequence(s) to match
+                * Custom mutagen sequences
         * Existing Project
             * Build a project List
                 * All available projects
                 * Matching projects using metadata
         * Merge Existing Projects
             * Build a project List
                 * All available projects
                 * Matching projects using metadata
     * Predefined Configuration File
 
 
 This is the default view of TAPDANCE in galaxy after clicking the link in the tool bar.  Each input item will be discussed below as well as any changes that may result in the view.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_default_view.png)
 top
 
 
 The first choice a user is presented with is whether they would like to define the project parameters using Galaxy or whether to upload and use a predefined config file.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_specify_or_predef.png)
 top
 
 
 There are three options for starting points in Galaxy, raw sequences, re-running a previous project or merging multiple existing projects.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_starting_point.png)
 top
 
 
 Choosing to start with sequences results in the following options.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_start_w_fastX.png)
 top
 
 
 There is a default value for the mutagen sequence, but it is a fairly narrow range of experiments it will be useful for.  TAPDANCE will attempt to match and strip the provided mutagen sequence(s) between the barcode and genomic sequence in the provided experimental sequences.  Any experimental sequences that do not match a mutagen sequence are not used in subsequent steps of the TAPDANCE process.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_mutagens.png)
+top
+
+
+Entering a custom sequence and its relavent help text
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_custom_mutagen.png)
 top

WikiPage Galaxy Options modified by Jesse Erdmann

Jesse Erdmann — Thu, 01 Dec 2011 20:36:58 -0000

--- v10 
+++ v11 
@@ -4,34 +4,40 @@
 * Specify options in Galaxy or use a predefined config file
     * Specify options in Galaxy
         * FastX
+            * Mutagen sequence(s) to match
         * Existing Project
             * Build a project List
                 * All available projects
                 * Matching projects using metadata
         * Merge Existing Projects
             * Build a project List
                 * All available projects
                 * Matching projects using metadata
     * Predefined Configuration File
 
 
 This is the default view of TAPDANCE in galaxy after clicking the link in the tool bar.  Each input item will be discussed below as well as any changes that may result in the view.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_default_view.png)
 top
 
 
 The first choice a user is presented with is whether they would like to define the project parameters using Galaxy or whether to upload and use a predefined config file.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_specify_or_predef.png)
 top
 
 
 There are three options for starting points in Galaxy, raw sequences, re-running a previous project or merging multiple existing projects.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_starting_point.png)
 top
 
 
 Choosing to start with sequences results in the following options.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_start_w_fastX.png)
+top
+
+
+There is a default value for the mutagen sequence, but it is a fairly narrow range of experiments it will be useful for.  TAPDANCE will attempt to match and strip the provided mutagen sequence(s) between the barcode and genomic sequence in the provided experimental sequences.  Any experimental sequences that do not match a mutagen sequence are not used in subsequent steps of the TAPDANCE process.
+![Default view](http://tapdancebio.sourceforge.net/screenshots/TAPDANCE_mutagens.png)
 top

WikiPage Galaxy Options modified by Jesse Erdmann

Jesse Erdmann — Thu, 01 Dec 2011 20:01:02 -0000

--- v9 
+++ v10 
@@ -45,17 +45,17 @@
 top
 
 
-When an existing project is the chosen starting point, the following options are available.
+To populate the list of projects to select from, the List TAPDANCE Projects tools needs to be invoked.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/List_projects.png)
 top
 
 
-When an existing project is the chosen starting point, the following options are available.
+The easiest route is to simply list all available projects.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/List_project_options.png)
 top
 
 
-When an existing project is the chosen starting point, the following options are available.
+If the list of available projects is impractically long, using metadata tags to filter the list returned is useful.  The returned list will only contain projects where at least one of the libraries had at least one of the tags entered on the form.
 ![Default view](http://tapdancebio.sourceforge.net/screenshots/List_project_add_tag.png)
 top