# HG changeset patch
# User trinity_ctat
# Date 1513111160 18000
# Node ID acff55f2d70ac2fab3a9ed48652afdea690c328a
# Parent  a2dc68c7fef6a2db1c20c06f8d500131f9331f24
Uploaded

diff -r a2dc68c7fef6 -r acff55f2d70a data_manager/add_ctat_ref_lib.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/add_ctat_ref_lib.xml	Tue Dec 12 15:39:20 2017 -0500
@@ -0,0 +1,37 @@
+<tool id="ctat_genome_ref_lib_data_manager" 
+    name="CTAT Genome Reference Library Data Manager" 
+    version="1.0.0" tool_type="manage_data">
+    <description>Retrieve, and/or Specify the location of, a CTAT Genome Reference Library. 
+    </description>
+    <requirements>
+        <requirement type="package" version="2.7">python</requirement>
+    </requirements>
+    <command detect_errors="default">
+        <![CDATA[
+        echo "Current directory and contents" && pwd && ls -la . &&
+        echo "Tool directory and contents are" && echo "$__tool_directory__" && ls -la "$__tool_directory__" &&
+        python add_ctat_ref_lib.py ${download}
+            --ref_genome "${genome_name}"
+            --destination_path "${destination}" 
+            -o "${out_file}"
+        ]]>
+    </command>
+    <inputs>
+        <param name="download" type="boolean" checked="false"
+             truevalue="--download" falsevalue="" label="Need to Download? (yes/no)" />
+        <param name="genome_name" type="text" label="Reference Genome name" />
+        <param name="destination" type="text" label="Local Destination (full path)" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <help>
+        Retrieve, and/or specify the location of, a CTAT Genome Reference Library.
+        When download is true, the file retrieved and processed is https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v26_CTAT_lib_Nov012017.plug-n-play.tar.gz.
+        Specify the Full Path of the location where the CTAT Reference Library should be placed.
+        You will need approximately 30GB of space for this library.
+        If you already have the library, 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 name will be used as the selector text of the entry in the data table.
+        For more information on CTAT Genome Reference Libraries, see <a http="https://github.com/FusionFilter/FusionFilter/wiki">FusionFilter</a>
+    </help>
+</tool>
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