# HG changeset patch
# User trinity_ctat
# Date 1540312947 14400
# Node ID 238636afb3e106a672557eb6a83e02f93dfa4d3b
# Parent  da412c8771bf16020fd513568fb13016e9890a24
Still working on Help text.

diff -r da412c8771bf -r 238636afb3e1 data_manager/add_ctat_resource_lib.xml
--- a/data_manager/add_ctat_resource_lib.xml	Tue Oct 23 12:19:20 2018 -0400
+++ b/data_manager/add_ctat_resource_lib.xml	Tue Oct 23 12:42:27 2018 -0400
@@ -162,58 +162,58 @@
     <outputs>
         <data name="out_file" format="data_manager_json" />
     </outputs>
-    <help><![CDATA[
+    <help>
         Retrieve, and/or specify the location of, a CTAT Genome Resource Library.
+        
         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.
-        The other options should be self-explanatory.
+           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.
+           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.
+           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 />
+           This assumes you already have a build library and need tell galaxy where it is.
+
         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 "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.
-        <br />
-        <strong>
-        If a download or a build is interrupted, re-running the job should pick up where it left off.
-        </strong>
-        <br />
+
+        **If a download or a build is interrupted, re-running the job should pick up where it left off.**
+
         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.
-        <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 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. 
-        <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 />
+        requiring a Genome Reference Library resource (ctat_genome_resource_libs).
+
         For more information on CTAT Genome Resource Libraries, 
         see https://github.com/FusionFilter/FusionFilter/wiki
-    ]]></help>
+    </help>
     <code file="add_ctat_resource_lib.py" />
 </tool>