diff data_manager/add_ctat_resource_lib.xml @ 49:c47ac2deaaf8 draft

Adding comments.

--- a/data_manager/add_ctat_resource_lib.xml	Thu Oct 25 21:44:51 2018 -0400
+++ b/data_manager/add_ctat_resource_lib.xml	Fri Oct 26 11:17:43 2018 -0400
@@ -1,6 +1,8 @@
 <tool id="ctat_genome_resource_libs_data_manager" 
     name="CTAT Genome Resource Libraries Data Manager" 
     version="2.0.0" tool_type="manage_data">
+    <!-- This Data Manager tool was written by Cicada Dennis of Indiana University for the Broad Institute.
+    -->
     <description>Retrieve, and/or specify the location of, a CTAT Genome Resource Library. 
     </description>
     <requirements>
@@ -60,16 +62,6 @@
         ]]>
     </command>
     <inputs>
-        <!-- The following are left in here, just as examples of various ways of doing options.
-            <param name="force_download" type="boolean" checked="false"
-                truevalue="- -force_download" falsevalue="" label="Force New Download? (yes/no)" />
-            <param name="download" type="select" label="Need to Download?">
-                <option value="single" selected="true">Single Dataset</option>
-                <option value="paired_collection">Paired Collection</option>
-            <when value="paired_collection">
-                 <param name="fastq_input" format="fastqsanger" type="data_collection" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
-            </when>
-        -->
         <conditional name="genome_resource_library">
             <param name="build_type" type="select" label="Download CTAT Genome Resource Library?">
                 <option value="download_and_build" selected="true">Download from CTAT and build if needed</option>
@@ -85,7 +77,7 @@
                      this data_manager.
                 This is the dynamic way to get the options filled.
                 <param name="filename" type="select" label="Select File" display="radio" 
-                    dynamic_options="get_ctat_genome_filenames()" 
+                    dynamic_options="get_ctat_genome_urls()" 
                     help="Select a CTAT Genome Resource Library to Download." />
                 Here is the static method for what is online in April 2017:
                 <param name="filename" type="select" label="Choose which library to download.">
@@ -157,7 +149,6 @@
                 <param name="cosmic_files_location" type="text" label="Location of the COSMIC files (See Tool Notes)." />
             </when>
         </conditional>
-        -->
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json" />
@@ -180,7 +171,7 @@
         All options allow the user to do a gmap_build on the library 
         and also to integrate ctat-mutation resources into the library.
 
-        You will need approximately 62GB of space for this library, once it is built, 
+        You will need approximately 62GB of space for a human genome resource library, once it is built, 
         but if downloading and building, to be safe provide at least 75GB.
 
         The installation of this tool takes some time, due to building a conda environment for the dependencies.
@@ -195,8 +186,8 @@
         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.
 
-        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 
+        Neither the "source_data" nor the "plug-n-play" versions have Mutation Resources included. 
+        Those must be downloaded separately and integrated into the Library. If you are going to be using the 
         ctat_mutations tool, check the Download Mutation Library check box.
 
         In order to integrate the Mutation Resources into a CTAT Genome Resource Library, you must have previously downloaded
@@ -210,7 +201,7 @@
         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 a Genome Reference Library resource (ctat_genome_resource_libs).
+        requiring a Genome Reference Library resource (These are stored in the ctat_genome_resource_libs table).
 
         For more information on CTAT Genome Resource Libraries, 
         see https://github.com/FusionFilter/FusionFilter/wiki