changeset 28:8ad5c63e4f87 draft

Adjusting Help. Making interface for Build Location consistent.

--- a/data_manager/add_ctat_resource_lib.xml	Sun Oct 21 21:40:51 2018 -0400
+++ b/data_manager/add_ctat_resource_lib.xml	Tue Oct 23 10:13:40 2018 -0400
@@ -25,7 +25,7 @@
               #if str( $genome_resource_library.rebuild ) == "true":
                 --new_library_build
               #end if
-              #if str( $genome_resource_library.specify_build_location.build_location ) == "different_location":
+              #if str( $genome_resource_library.specify_build_location.build_location ) == "true":
                   --build_location="${genome_resource_library.specify_build_location.different_build_location}"
               #end if
             #elif str( $genome_resource_library.build_type ) == "build_from_source":
@@ -117,14 +117,8 @@
                 <param name="keep_archive" type="boolean" checked="true" label="Keep downloaded archive rather than deleting after build?" />
                 <param name="rebuild" type="boolean" checked="false" label="Force new build of Library?" />
                 <conditional name="specify_build_location">
-                    <param name="build_location" type="select" label="Location of Built Library">
-                        <option value="same_as_download" selected="true">Build in Download location</option>
-                        <option value="different_location">Build in a different location</option>
-                    </param>
-                    <when value="same_as_download">
-                        <!-- do nothing here -->
-                    </when>
-                    <when value="different_location">
+                    <param name="build_location" type="boolean" checked="false" label="Is the build location different than the source location?" />
+                    <when value="true">
                         <param name="different_build_location" type="text" label="Build Location (full path)" />
                     </when>
                 </conditional>
@@ -170,34 +164,57 @@
     </outputs>
     <help>
         Retrieve, and/or specify the location of, a CTAT Genome Resource Library.
-        When download is true, the files at https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/
-        are used as selectors for the user to choose among.
+        There are three options: 1) Download from CTAT and build if needed;
+        2) Build library from local source data; 3) Specify location of built library.
+        1) Download from CTAT and build if needed: 
+        This option uses the files at https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/
+        as selectors for the user to choose among.
         Specify the Full Path of the location where the CTAT Genome Resource Library should be placed.
-        You will need approximately 62GB of space for this library.
+        The other options should be self-explanatory.
+        2) Build library from local source data:
+        This assumes that you have already downloaded the source data for a build and you want to build it.
+        3) Specify location of built library:
+        This assumes you already have a build library and need tell galaxy where it is.
+        <br />
+        All options allow the user to do a gmap_build on the library 
+        and also to integrate ctat-mutation resources into the library.
+        <br />
+        You will need approximately 62GB of space for this library, once it is built, 
+        but if downloading and building, to be safe provide at least 75GB.
+        <br />
         The installation of this tool takes some time, due to building a conda environment for the dependencies.
-        The download extracts the files during the download. The "source_data" files download faster, but then must be built.
+        The "source_data" files download faster, but then must be built.
         Building the library from the "source_data" files can take many hours, depending on the resources of your machine.
         The "plug-n-play" can take considerable time to download, depending on your internet connection. Even with high speed,
         it is about 25GB that is transfered, so plan accordingly.
         If you have a good speed internet connection, downloading the plug-n-play will usually be faster than building.
-        If a download or the build is interupted, re-running the job should pick up where it left off.
+        <br />
+        <strong>
+        If a download or a build is interrupted, re-running the job should pick up where it left off.
+        </strong>
+        <br />
         Neither the "source_data" nor the "plug-n-play" versions have had their gmap index built. If you are not going to be
         using gmap_fusion, then you can uncheck the gmap_build check box and save the space and time building the index consumes.
+        <br />
         Neither the "source_data" nor the "plug-n-play" versions have mutation resources included. Those must be downloaded
         separately. By default the Mutation Resources are not integrated into the Library. If you are going to be using the 
-        ctat_mutations tool, check the Download Mutation Library check box. 
+        ctat_mutations tool, check the Download Mutation Library check box.
+        <br />
         In order to integrate the Mutation Resources into a CTAT Genome Resource Library, you must have previously downloaded
-        COSMIC resources (See Step 2 from 
-        <a href="https://github.com/NCIP/ctat-mutations/tree/master/mutation_lib_prep">Mutation Lib Prep Information</a>.)
+        COSMIC resources (See Step 2 from https://github.com/NCIP/ctat-mutations/tree/master/mutation_lib_prep )
         You can place them directly into the Genome Resource Library location, or if the Library is 
         not built yet, or you do not know the full path to it, specify the directory where the COSMIC files are, so they can be 
-        integrated into the Library. The Mouse genome is not currently supported in ctat_mutations.
-        If you already have a CTAT Genome Resource library installed on your system, 
-        specify the full path of the location where it exists and leave the download box unchecked.
-        The Reference Genome name may be left empty if downloading. 
-        The filename will then be used as the selector text of the entry in the data table.
+        integrated into the Library. 
+        <br />
+        The Mouse genome is not currently supported by ctat_mutations.
+        <br />
+        If the Reference Genome Display Name is left empty a name will be created, 
+        but any text that will best guide the user can be entered here. 
+        It will be the text that is used for selecting the library in pull down lists 
+        requiring the Genome Reference Library resource.
+        <br />
         For more information on CTAT Genome Resource Libraries, 
-        see <a href="https://github.com/FusionFilter/FusionFilter/wiki">FusionFilter</a>
+        see https://github.com/FusionFilter/FusionFilter/wiki
     </help>
     <code file="add_ctat_resource_lib.py" />
 </tool>